Does the game punish you if you want to set up a team that runs/passes the ball 90% of the time. I don't mean opponents' gaming to stop either one, but some kind of game "penalty" for one-sided use of either?

Just overuse of single plays, so if you want an all run gameplan, as long you have 15-20 run plays you would probably be ok, but if you only use 3 over and over it would get in trouble. But if the opponent game plans appropriately and plays for an all run or all pass it could struggle regardless, but it won’t be because of “overuse”

Defense focus automatically switches to run or pass against a play once the defense has seen the play three times even if no overuse appears in the play by play and the defense gains a bonus against the past. Overuse only appears in the play by play if the defensive bonus directly contributes to the result.

Same for offense versus defensive plays.