I believe that this engine favors the "balanced formations"...Pro Set and I-Formation. My belief is that it was designed with these in mind and then "expanded outwards" to allow for variations...Trips and Shotgun on one end....and NDBox and Wishbone on the other.
I would suggest that you do not pick formations based on what level you are playing at. I suggest you pick what you want to run, learn how to run them and carry them with you wherever you go.
The key to using all these different formations is that they require different personnel. Shotgun/Trips needs GREAT QB and a bunch of WRs. NDBox needs beast RBs and TEs, not so much is the QB needed. Pro Set and I-Formation require the whole package, QB, RBs, TE, WRs. ALL OF THEM need great OLs. So, it is tough to play Shotgun and Wishbone equally well. (Not to mention FIQ).
My D3 team was Trips and I-formation my whole career there until about 4 seasons before the 3.0 launch...I had just switched over to the All Shotgun approach. Since 3.0, I have gone to a Pro Set, Trips, Shotgun mix. Season 1 was all Shotgun, but mostly running. Season 2 was mostly Shotgun, with more passing, Season 3 was mostly Pro Set and Trips. This season will be a mix of all three. I'm still experimenting with what works best.
Regarding the wishbone, I'm still using it at D1AA, but not sure that I will keep it nor not. I've got a very talented team and it still does not produce like it used to in 2.0. My defense has been playing very well (but I'm also in an ALL SIM conference right now) and that is what has kept this team from being another disappointment.