You have not explained what your actual goal is, beyond just using a computer that runs linux -- which apparently you've already been doing anyway for ~10 years.
To be totally honest (since this is definitely an "opinion based" question), all the fussing with different distros borderline absurd. This is not to say they aren't different in superficial ways, but they are NOT fundamentally different. The differences that are most significant are the ones that are most immutable, which often includes the init system, and pretty much always the package management system.
You refer to programming type activities a bit, but also to the fact that you are wary of investing too much time in them. If you primarily use a computer in order to be productive in some realm (again, you haven't said anything about this)1, avoid programming as much as you can and instead focus on the use of existing software that will assist you in being productive. If you need to do a lot of word processing, you want to hone your proficiency with word processors, not programming.
I like to come back to the Linux world but I'm afraid of putting a lot of time there.
Linux is not a fast food culture, period. I'm not saying this to denigrate fast food. Everybody likes to eat, but not everybody enjoys cooking. Likewise, most people enjoy listening to music of some sort, but when push comes to shove, most people actually do not enjoy making music.
Cooking well or playing an instrument requires a significant investment of time. It is not necessary that everyone do it. My advice, if you are already comfortable and happy with Windows, is to stick with that. You've obviously had linux at your disposal for a long time and yet never really taken to it.
B. Using Windows (as host) and installing Linux on a virtual machine C.
Please, NO. Again, you have not explained what the possible purpose of this would be, but maintaining a VM image just so you can use OS Whatever to do whatever general purpose computing tasks is not just borderline absurd, it is right over the top completely ridiculous. VMs are useful for testing, emulation, and containment. Using them as places to just "do stuff" that doesn't require a VM (and more than likely, is negatively impacted and complicated by doing it in a VM) is like running your car in the driveway so you can listen to the CD player.
1. You do mention a "scientific background" but you don't refer to how this involves the use of a computer. Are you using it to do science? What kind of science? How? Etc.
[Post OP Revision]
Okay, so now we have some more concrete things to work with. Your primary list of applications is straightforward: MATLAB, Python, C/C++, TeX, PDF, Git and (my extrapolation) Java. These are going to work equally well on any mainstream linux variant. There's simply no way someone can (rationally) claim Java or Tex or any other of those things work better on one distro vs. another. But keep reading.
Part of the reason they're all equivalent in this sense is that all of them use the same kernel (technically, "Linux" is just the kernel) and the same fundamental userspace (by which I mostly mean, the C library, which is a critical part of everything). They each configure and compile the kernel individually, and even maintain their own set of patches, but these are not hugely significant. For example, if a patch really makes the difference between a piece of hardware working and not working, that is going to end up in the original source tree; it is not something that only one distro offers.
If you do have problems with a distro kernel as configured, the solution is not to keep switching distros until you find one that works out. The solution is to configure and compile a kernel yourself. This will be very tedious the first time, but it is not beyond the capabilities of an adult, literate user. You can either use the vanilla source, or you can use a source package provided by the distro.
"Research Suites" are not something I know much about, but I think the same logic will apply (they will work equally well on any distro), particularly if they are Java based.1 There is a Scientific Linux distribution that is a repackaging of Redhat, much like CentOS. It's maintained and used by CERN, so presumably works, but just because it is called "Scientific" does not necessarily mean it is going to be any better or worse for your purposes. The reason CERN does this is not because they need to run software that doesn't work equally well on, e.g., Ubuntu. They do it:
So they can have a standardized platform.
So they can gatekeep that standardized platform. For example, they could have just decided at some point to use CentOS. However, it's necessary to keep the systems up to date, presumably in parallel. Let's say one day the regular distro updates introduce some minor snag that causes someone to miss their day on the particle accelerator -- unhappy scientists! Maintaining their own distro is not a guarantee against this (there are no such guarantees, of course), but it does put the power in their hands.
That said, distros which parallel Redhat tend to be behind the times by a year or so. This is not necessarily a bad thing, the justification being stability, but for an independent user it is sort of pointless. Generally speaking, the system improves with time, and in the context of a single computer owned and operated by you for you, any problems resulting from not standing back far enough from the present are probably easily rectified (to extend the metaphor, you can always take a step back when necessary).
I don't have any problems with user interface of Linux or command
lines or manuals etc. These are things which I actually love. I'm
afraid of putting LOTS OF TIME in Fixing Buggy and Broken Packages/OS...
I've been a linux user since the last century. For the past half dozen years or so, I've been working full time on linux systems, mostly by choice, mostly engaged in programming. My distro of choice currently is Fedora, meaning, if someone asks me what I want set up on a server, I say Fedora. But usually what they really say is that they've set the server up with Ubuntu or Debian, lol. I'm perfectly comfortable with that and don't consider "Fedora vs. Ubuntu" (e.g.) a serious argument. I've also tried out various other distros for myself, notably Gentoo which I was my primary distro for several years.
Meaning, if you want to use it effectively, you are probably going to have to put in much more time than you would with more mainstream operating systems. In this ongoing process, you are, without doubt, going to hit ridiculously frustrating roadblocks. In my experience, that never ends, but I am sure my patience and ability to solve problems (in this context) has improved. Part of solving problems is identifying them correctly, so let's examine your complaint about "Fixing Buggy and Broken Packages" and the time it wastes.
Complaints of that sort almost always boil down to user ignorance and confusion. Of all the thousands upon thousands of hours I have spent wrestling with the system, 99% of it has been necessary because I had to learn something, and maybe 1% because of genuine defects. Of course, particularly during the first few years, I did not always see it this way. A great way to learn the difference is to file a bug report when you think that really is the problem, heh-heh. Yes, you have to create an account somewhere and respond to emails, but if you are serious, you might as well act that way.
Part of the reason that user confusion often ends up getting resolved in bug reports in the linux world is that, unlike with commercial products, the authors of the software may not have much incentive to get you to use or understand it.2 If you have problems using it, there's no reason it should matter to them at all. Ideologues of a certain stripe will argue this is sure to result in an inferior product; IMO it actually results in a superior one, which comes back to why I love linux but don't recommend it to others: I don't want a product that caters to a lowest common denominator. I think it's great that my 74 year old, hopelessly technically inept mother enjoys her iphone. But the things that make it usable for her make it very un-useful for me. That's the nature of the beast.
Because of this linux sometimes seems a little "mean". Like, here's this awesome looking system with all of this potential and so on, but I have to waste a freaking day trying to figure out how to configure my desktop?? I've been there and I've wanted to hunt down and strangle the people I consider responsible. How can they be so callous? Why can't they just make this easier in obvious (to me...) ways? At least some better documentation!
Part of the issue there is resources. People developing FOSS software generally do not have much, or any, budget. They can't run out and hire a team of technical writers to document the product, and sadly, it's not something people are keen to volunteer for: they want to code. Finding good documenters may be harder than finding good programmers. It's just not rewarding in the same sense when you aren't being paid.
IMO, linux is a platform by technical people for technical people (which is obviously part of the reason you are interested). To be fair, there is a lot of effort, particularly by GNU and Canonical, to make it generally palatable as an alternative to mainstream operating systems for people in parts of the world where handing hundreds of dollars to MS or Apple every few years is a serious issue. Which is terrific, but it's still primarily a technical platform for technical people.
So, returning to some of the stumbling blocks: Not everyone cares about the ideals of free (not as in beer) open source software and it is easy to regard the system from an end user perspective as essentially the same kind of thing as a proprietary OS. This is a mistake, not because I think you need to care about FOSS ideology, but because there are some substantial pragmatic differences in a context where anyone is welcome to contribute (note, this is not synonymous with being taken seriously; that depends on what you actually bring to the table) and (as already explained) no one is really obliged to answer to the user or any other particular authority. The "linux world" is in many ways anarchistic (in the philosophical sense, not the colloquial one meaning "chaos"), except that many of the predominant organizations (e.g. GNU, Redhat, Cannonical) are normative hierarchies.
Again, I'm not saying you need to take any particular kind of ideology seriously, etc. I'm pointing this out because it is pragmatically useful to understand. As a linux user, YOU are part of the project to a much greater extent than the average user of the big proprietary OS's. This is why stuff like bug reporting is significant, although again, it is unfortunate that that is where a lot of critical interaction ends up taking place. Much better to do it here, of course!
I'm also not saying you are "part of the project" because I think that a sense of community is a nice thing or because linux geeks are all secretly (or not so secretly) hippies or because it might make a good marketing slogan. I'm saying it because the project requires work and you need to see yourself as part of that work (rather than as a consumer of it) if you want to get the most out of the experience, pragmatically speaking.
Or you can find a wall and bang your head against it. Nobody cares, honestly. That's freedom.
I've installed Fedora (SUSE) and I want to adapt KDE(Gnome) as my primary DE, but the default configuration provided in precompiled packages is very buggy and fail prone
You refer to the fact that you do a little programming, so I am sure you are familiar with the situation where a neophyte looking for help says something like, "My compiler's std::string doesn't work properly!". I've spent a lot of time helping people with programming problems and complaints about how the compiler must be buggy, etc, are almost always (as in, upwards of 99% again) mistaken.
Just like issues with the kernel, resolving problems with configuration is usually not best accomplished by switching distros, it's by changing the configuration. Meaning, you have to learn about it in the context I've already described. You express a lot of frustration with the time this takes -- everybody feels this way, but that is the nature of the beast. It's not a product that has been sold to you with a set of promises, and (again) approaching it that way will not help. Switching distros out of frustration is giving up; I've done it, and in the long run I don't think it accomplishes much beyond soothing the momentary anger at the __ing __heads who put you in this situation. Eventually you have to sit down and accept that if you want something your way you may have to do it yourself.
Okay! So here's a few suggestions:
Fedora. My fav, as I've said, but you seem to have had some bad experiences. Fedora/Redhat differs from Ubuntu/Canonical in that they focus their resources less on the desktop -- there's no parallel to Unity, for example. Fedora tends to be the most up to date distro (but this is not the case with the downstream RHEL and derivatives, as discussed).
Ubuntu. By intention, this is probably the most conventionally user friendly distro, and not surprisingly, the most popular. Ubuntu generally stays more or less as up to date as Fedora, perhaps complicated by its relationship to the more conservative Debian.
Arch. I have only tried Arch out for a short period of time but take it on credit from others that it is stable over the long term. The reason I recommend this is because I think it would have been a great experience for me at one point, if it had existed years earlier. Being more hands on, it seems like a good way to (have to) learn things you might otherwise avoid. So, that probably means more frustrations; hopefully I've made the point that dealing with these head on takes time but will probably lead to a happier you. Maybe not later this afternoon, but eventually.
I haven't left out other distros here because I think they suck, etc. I work with Debian everyday, for example, and have no serious issues with it in relation to any of the above. But those are my top three recommendations.
You're a PhD student who does serious work with a computer. Given an infinite amount of time, most people would like to do a lot of things they don't have time for in reality.3 That's life. I think you should continue to work with linux, but you obviously need to balance the demands of that with your academic obligations. It is better to recognize what you don't have time for than to pretend that you can get those things done properly without sufficient time, which is why I originally suggested you might be better off sticking with Windows. Frustration is natural, but lamenting these facts won't change them: some things simply require serious time and effort, which is why I originally said that the distro you choose won't make that much difference. They're all still linux, and linux is a very serious beast :]
1. It's worth noting that you are not confined to the distro java. You can install the latest Oracle and configure the system to use that if you want or need to.
2. But they do have a real incentive to resolve bug reports! Note I am not recommending this as a way to bug devs unless you genuinely believe there is a bug.
3. Remember how I said originally most people love food and music, but not necessarily cooking and playing an instrument? It's because they're mortals ;)