Just want to share my experience and how I eradicated the choppy animations.
Bought a brand new rMBP (2.7 ghz i7, 16GB ram, 512ssd) and wasn't happy with the choppy animations after spending a ridiculous amount on it. So, after a lot of digging I found this (don't do it yet) - How to fix Intel HD and Nvidia's choppy graphic ... - YouTube. That kinda of helped initially but I just didn't like doing something like that to my machine, so I just started again with a fresh install of ML.
I booted in recovery mode (command-R), started disk utitily and PARITIONED - not erased - my drive with 1 partition using the GUID option which is in advanced options I think. After it finished that (was super quick) I then reinstalled ML back in the recovery mode window.
Something I noticed when I initially set up my computer is that when I tried to install the updates they did appear for a while, but then stopped halfway through, I then restarted the app store to try again but the updates dissapeared. From some more digging I think, think it might be to do with apple keeping track of what updates I had previously installed (on my old mbp) so when I clean installed it this time I chose not to to log into iCloud in the installation and wait until I did all the updates the app store said I needed.
After all that my machine is now how I wanted it to be, super smooth scrolling everywhere (apart from a few websites, Facebook is definitely the worse), desktop switching, and mission control. I have disabled automatic graphics switching (I don't use it to it's full potential anyway, only running Logic, adobe suite etc) so I am using the big daddy graphics card, but everything is super smooth (espeically the option-tab application switch going to diff desktop, which really bugged me) and I'm finally happy with it.
I hope this will help some of you 🙂