Indiana don't get enough penetration in their halfcourt offense. Allow the defense to stay in between the ball and hoop. Don't force them off-balance often enough. Leads to a lot of low to medium percentage shot attempts.
Defensively, their interior defense isn't strong enough to handle slashers like Wade and LeBron consistently over a seven game series. Hibbert is too slow and immobile and none of their other bigs provide any sort of rim protection.
If Miami moved Bosh to center (against Hibbert) and played small, they'd run Indiana right off the court. A four game sweep. Unfortunately, Spoelstra continues to refuse to do that and plays less effective lineups instead so it'll drag out another game or two before Miami finishes them off.
Miami will always have another gear that Indiana simply can't match. The Pacers just don't have the talent to do it.