The only legitimate beef people can really claim is the EJ pick, imo.
But, the Bills were forced into a QB pick, traded down, picked up an extra pick (who turned into Kiko/Shady, I think?), and still got the guy they wanted. It's not like that QB class was super great (unless I'm forgetting someone?).
Other than that, I can't see how anyone can complain. I guess you can hindsight OBJ instead of Sammy, but OBJ wasn't rated nearly that high from what I remember, and we were looking at Ebron if we didn't trade.
I'm not sure if it's realistic to expect a GM to hit a homerun on every draft pick, but I think Whaley has done a good job building talent for this team. Our problems lie with coaching and injuries at this point.