Whenever I switch my window focus (i.e. Nautilus to System Monitor) it takes much longer than it should. I click, and then it switches after ~1 sec. Using System Monitor I noticed a larger than normal jump in CPU usage when switching windows. It seems to be prevalent for all applications.
CPU: i3-4170, using the microcode firmware
GPU: Nvidia GTX 950, running proprietary drivers
I'm also seeing this on 16.04 with i5-4460 and a GTX 960 on a 32bit system (don't ask!) I don't see it with nouveau drivers but I do with the NVidia proprietary ones (all I've tested up to 381.13.)
Probably the same issue as CPU spikes and performance problems changing window focus in Unity/Ubuntu 16.04.2.
Although not a proper solution, restarting unity by using unity --replace seems to work around the issue for that session. (You might need to try it again if it doesn't work first time.)
This could be related to bugs.launchpad.net/ubuntu/+source/unity/+bug/1300892. If you think that bug affects you then please do click "This bug affects me" at the top so that the maintainers get a good reflection of how many people this bug impacts as this is currently triaged as a low priority bug.
EDIT: It seems that adding the command /usr/bin/unity --replace command to "Startup Applications" does work okay as a kludgy but less temporary workaround. :)
