As far as the difference between airplanes, The TC-12 is bigger, faster, longer range.
As far as squadron differences, VT-35 is unquestionably the way to go.
The leadership at 35 is awsome, its defenitly the best squadron in the navy.
I have never.. ever.. heard a 35 guy say he wishes he was in 31, but I hear it from 31 guys /all the time/.
The type rating bit.. who cares.. its all about the culture, and the VT-35 culture is top notch.
In response to Kray, as far as I know, C-130 Marines only go to VT-31, the 35 slots are just Osprey dudes.