With Nautilus, new drives appear on top but not focused, as you say ... and I think this is OK because it means a new window doesn't steal your input focus when you're in the middle of typing.
With Eclipse, now that you mention it, when it hits a breakpoint you'd expect Eclipse to come to the foreground but it doesn't.
With some apps it does work - clicking hyperlinks brings Firefox to the foreground & focused.
I think this is a form of "focus stealing" prevention. See e.g. elliotth's blog: GNOME "focus stealing prevention" a sick joke
But fwiw I don't think this is a problem specific to gnome. I've had similar problems on Windows in various situations.
I don't agree with all of that article I linked above, but the main point is right: it's due to poor, even sloppy, application design. So maybe the solution is a heavily-customisable focus-allowing filter tool. "If app x has focus and app y requests it, allow, if app z has focus app q requests it, deny".