It just really dragged for that last half. The ending was also bleh and seemed really stupid to me (the whole Batsy on the run thing for murder, just dumb and made no sense no matter how you slice it).
I would imagine the reason Batman took the fall for Dent was because Dent took the fall for Batman earlier in the movie.
Dent's reputation had to be maintained in order to keep the convicted cons/mafia in prison. If what Dent did as Two-Face got out then his credibility would be harmed and it'd endanger the convictions on the mafia guys.
Batman had to take a "fall" with his reputation to maintain Harvey's (and possibly as "payment" for taking a life.)