While I agree that system QBs are sometimes not given proper credit for their talent and within their system, I think you also have to give some other players the benefit of the doubt that they could flourish equally well if placed in the same system. When players like Brennan fail to get proper attention in Heisman races, etc, I think it usually has more to do with the "mid-majors" for which they play than the system in which they play.
Also, I think the issue is much less pronounced at the FCS level, in the sense that there isn't as big of a perceived difference between the haves and the have nots. I think FCS "system" players or more likely to be considered on equal footing for individual awards than "system" players at the FBS level.