Yeah that's true, I think the premise for the system comes from FIFA, so that's likely how it works.
http://www.ea.com/fifa11/videos/ca03...001065140aRCRD
I am interested to so this translates exactly into the the game. The thing I like most about it is that it seems to encourage no wasted movement on the field, which has been desperately needed in football games. I would presume as long as you utilize players within their wheelhouse, according to their stamina rating, you should be good. For instance a highly athletic QB like RG3 will likely be able to scramble around, within reason and still recover between plays, whereas trying that with Payton Manning will tire him out far more. Not to the extent of Manning coming off the field but his performance being noticeably effected and more prone to injury. I'd imagine since OLineman can't even be User controlled except on INT returns and that don't spend much time deep running deep down field, the effects of fatigue on them will be realistically negligible.
So I think #2 is likely, maybe with some kind of feature where players request to come out, like I think it is in FIFA. I don't really understand the manipulation aspect for a CB you are referring to unless you are talking about people subbing in decoy receivers just to tire out starting CBs, which is a possible tactic. This might all somehow tie into Dynasty mode, so they are waiting til then to explain more.