To answer some questions:

LCB has priority to cover WR1 and RCB has priority to cover WR2. Matchups are not straightforward though, and change from play to play. For example, formations, blitzes, double coverage, all effect match ups on a play-by-play basis.

There is a balance between being able to control things at infinite detail and keeping the game easy enough to play. Different people will have different preferences for that balance. An option to include a TE in empty backfield sets has been requested, and we'll probably add that at some point.

There are a couple of reasons why we limit substitutions on offence. One is that this is a data driven game. We don't have much data on most WR running out of the backfield. The other reason is that in our initial testing some players found some unrealistic formations that gave unexpected advantages. Limiting where skill players can be lined up solved both problems.