here is the thing. you see the pats "99 ovr defense", but what does that really mean? it means they have depth. now, if you want to compare STARTING squads, most teams in the game can easily stack up (and in many cases surpass) the patriots. for instance, the jaguars and panthers have a better STARTING defense than the pats (if you go by the numbers). the 49ers have a very good starting defense. but because many teams don't have depth (the 49ers, for instance, drop down to a 71 ovr defense because our 2nd stringers are so terrible).
don't kid yourself though. the defense in madden this year is VERY good, even for "bad" teams. if you play disciplined D you will have success.
slo, try out some different playbooks. before you push start on the team select screen, press Y. you can pick from ANY of the playbooks in the league. for the colts, try out Pass Balanced. You may find it fits your style better (if you dont like a downfield passing game).