What if you want to use different layouts per applications? What if you have more than 2 layouts? One of the most annoying bugs for many people (not for me though) is now closing for the upcoming GNOME 3.8 release.
Control Center 3.8 introduces a new option to allows us to use different sources for each window.
Input Sources per Window
I am not sure when this bug came up, but I think it was in GNOME 3.6. Anyway, it will be gone in a few months with the next major release of GNOME.
If you want to learn more about it, just go ahead and read bug #684210 report with all details and developers opinions about it. iBus in GNOME is one of the most discussed topics ever ;)