Here are my thoughts: DBs should not have the same coverage and WRs should not have the same catch ratings, you're correct. That said, you have to fudge some ratings due to the inconsistencies in the game engine. If certain ratings are lowered below a specific point, the player plays like complete crap. Personally, I don't feel coverage ratings should be lower than 85-90 for any DB, and likewise the catch rating for WRs. They should both be set between 85-90 and 127 for all players. Although RB's and maybe even some TE's who are not known as receivers can be lower than that.
It would be nice to be able to just drop everyone's ratings 40% across the board and expect the game play better, but again that's not possible due to the funky game engine. Some ratings you can do that with: you're dropping Agility for example and that should be fine. Although you might want to consider a tiered approach: 20% for RBs, WRs and DBs; 30% for TEs and LBs; 40% for everyone else... something like that.