You are all missing three major points.
#1: The NCAA simulation engine DOES NOT WORK ON A RELATIVE BASIS. The simulation engine determines simmed game statistics for positions such as QB, WR, and K based on absolute key positional ratings (OVR, AWR, CTH, KPW, KAC, etc.). These ratings are essentially broken later in dynasty mode. Therefore, the simulation engine does not compensate for the lower ratings across the board and lowers the statistical output of every player with poor ratings.
#2: The NCAA gameplay engine DOES NOT "always" WORK ON A RELATIVE BASIS. CPU controlled players with poor AWR simply do not perform intelligently on the field at most positions. This is simple to test... go create a team of all 99 AWR and watch them perform like professional football players and then go create a team of all 50 AWR players and watch them play like Pop Warner players. QB's in this game live and die by AWR. WR's without skill ratings are less useful than CB's. LB's without AWR will cost defenses points on a consistent basis. The only situations where gameplay plays out on a relative basis are 1-on-1 matchups such as OL/DL, WR/CB, and in tackling situations.
#3: The FCS teams do not regress. They eventually catch up in talent with the D-1 FBS schools and in some cases become more talented. Why? Because their players were created by the roster makers and actually have AWR and skill ratings. Can anyone really sit there with a straight face and claim that "everything's alright because everyone has the problem" while quality FBS schools are being trounced by FCS schools?
Simply claiming that "it's a level playing field" ignores all of the above. It also reeks of complacency. There is a problem with dynasty mode and we have at least one more patch to get this addressed. We don't "have to work with this". I can't speak for others, but if EA came out and said that they would not address this in a patch then I'd be selling my copy of the game immediately. Dynasty mode is the only reason that some people buy this game.