I am experiencing the same really annoying issue. The UI gets more and more slowly over time. When I restart, everything is super smooth, even when I open 10 hungry apps right away. After a while, the performance decreases, and even if I quit every app except for one, the mission control is still really really slow.
Since the lag is building itself up over time and it seems to happen as well on retina MacBooks, 17"-non-Retina-MacBooks (such as mine), and even retina iMacs with really fast hardware, it seems unlikely to be a hardware issue, but has to rather be some programming bug.
Disabling the transparency in the settings performs a miracle, but unfortunately I can't enable it without also checking the increase contrast checkbox, which makes the UI look quite ugly in my opinion, and isn't really a worthy trade for a faster mission control.
I have done a fresh Yosemite install, without much success. Also I have tried the resetting-the-PRAM-and-deleting-some-files fix previously mentioned- no success. It all seems to work, but I suppose it is merely the effect of the system restart.
I would like to ask if someone who had success with the fresh-install-of-yosemite fix did restore his system afterwards using time machine, or not.
When I did my fresh install, I was wondering if maybe the files that were causing the issue were restored when I restored my user from time machine. I did not click on "restore system from time machine backup", but instead I installed yosemite from scratch, and then when it asked me to create a user, I said restore personal documents and Applications from my time machine backup.
Do you think I could fix the issue by doing another fresh install of yosemite, but then create a new user instead of restoring my old one? I would have to migrate all my files, documents and applications manually, so it would be a ton of work which I don't want to do unless it has a good chance of success...