The default GNOME3 themes are a disaster for tiny screens. However, the Gnome3 crowd seems to be pretty unwilling to listen to their users. They only think of how stuff looks, in particular on a tablet PC or mobile device, it seems. Soon, Gnome3 will require a 4k screen.
Anyway, the best solution I have found is to switch the theme to the XFCE themes. On Ubuntu and Debian you should be able to install them via
apt install gtk3-engines-xfce gtk2-engines-xfce. Then you can use the
gnome-tweak-tool to change the theme. I'm currently using
XFCE-orange theme, and it has much less padding than the default Gnome3 desaster "Adwaita". Plus, it doesn't use that depressing black for half of the applications! I think the tooltips in Eclipse were also broken with Adwaita.
I'm slowly switching from Gnome3 to XFCE on my computers, one after another. Because Gnome3 keeps on getting less and less useful for me, as I'm not your average "joe clueless" user that the Gnome3 people consider to be their only audience. I'm fed up with them breaking things for me. Now they've just announced to discontinue the panel which I'm using instead of the broken by design gnome-shell.
For eclipse specifically, I suggest to
~/.profile. GTK3 with Eclipse is just a crazy waste of screen space.