The right/left could be kept for running plays, and why not say the ball is in the middle of the field on every play for simplicity reasons? It would be no different than what we currently have, but the right left would allow for more individual matchups, more strategy in setting depth charts, more advantage to having depth, MORE CONTROL! Which is what everyone is asking for.
As far as routes or individual plays for a playbook I think something like this could work. If I have a little guy with great hands and great elusiveness (WesWelker) I could have him run mostly short routes which could be a drop down. If you chose short you would understand your WR would be running a drag, quick hit, or slant. If I have a guy who has good but not great elusiveness and has good but not great speed (Hines Ward 3 years ago) I could set him to medium routes an 8 yard comeback, in, or out. If I have a burner (Mike Wallace) I could set him to deep routes a fly, post, or skinny post. If you have a Larry Fitzgerald or Andre Johnson then he can do everything and thus becomes difficult to cover, and will most likely win his matchup as he should.
As far as the corner lined up with him you could have 3 settings of tight, balanced, or cushion. Against Welker maybe you play tight to disrupt timing and knock him off his route, but if the coach has him running a deep route against you that play you may get burned. Against Ward depending on the skill of your DB you can play him however you see fit. Against Wallace you could play with a cushion, or if you know you have 2 blitzing LBs on that particular play you may play tight to keep him from getting a free release and getting into his deep route.
As far as defensive depth chart I think you need to be able to set your DB to cover a specific WR from the other team. The issue with WR#1, WR#2, etc. is that coaches hide their WRs by putting WR#1 in the #3 slot and we don't know until the second half and there is no saying he won't change where they line up.