After asking a lot of people, this is what seems to be the common answer:
"The small fan motor has a smaller flywheel. It can get up to speed faster, which is good for smaller tracks and tracks with tighter turns, where you do a lot of braking. The big fan motor has a bigger flywheel, which is beneficial at larger tracks where you are drafting and using the brakes less because it allows you to maintain more momentum."
Redhead Racing had this insight:
" I do know an engine with a bore on it does better at plate tracks then a stock block.... with that being said if you have one of the new big fan motors you?re less likely to have a bore on it unless you paid extra to have done so!  therefore by that math and older small fly wheel engine would be better At a plate track..."
Feel free to add your experiences. I think it is a very interesting topic!
Steve