Let's collect the suggestions for defense in one place. There have been some excellent ones in other threads 9e.g defensive packages based on offensive personnel is an excellent one).
I have two thoughts to kick this off:
1. A new "key" command: Key on TE. The defensive player would read the TE's block or route and either attack the run or go man-to-man on the TE (or, I suppose, drop into a zone).
2. A more robust "Run Rush" command. I don't mind the offensive line winning the battle, but the whole shoving a DL back into the secondary is just weird. I'd also like to see DL stats (particularly STR and AGL) heavily rewarded: if a DT is stronger than an OG then a DT in run rush should be hard to move.