I have a 2011 MBP, and I also get that choppy animation when switching full screen apps, but the weird this is, it only happens when my MBP is connected to my external monitor.
I have a 2012 MBA and this has happened ever since I bought it using both Lion and Mountain Lion. This is really not something you should have to deal with when shelling out the cash for a premium laptop. This is stuff that I only thought happend on 2-year old $500 HPs.