What player is "better" depends on what skills you value in the position based on how you play Madden and what kind of team you want to build, which is what the scheme-specific OVR attempts to reflect. If you're playing a 4-3, you wouldn't want to sign Chris Canty (a veteran 3-4 defensive end) as your 4-3 pass rush right end, for example, and the scheme-specific OVR calculation change for the 4-3 Edge Rusher setting reflects that. If you are constantly changing the position-specific scheme setting, you are misunderstanding the intention of the feature.
The OVR rating has zero effect on football gameplay anyway, it only affects the CPU valuation of players for depth chart sorting and team-building purposes.
CFM from top to bottom is designed around accruing and spending XP to progress. Any hopes that it be gutted out of the game are IMO entirely misplaced; EA would basically have to rip out CFM from the game and replace it with something else, and that isn't going to happen anytime soon by my estimation.