Actually Bruce getting back to Gotham made sense to me because we were shown in Begins that he has disguised himself, snuck on ships, walked on ice and is a ninja. We also saw people of high importance sneak into Gotham in trucks. To me it was always common sense. There's even concept art that shows Bruce walking the ice into Gotham. He "has a way to get in and out of the city" he says something like this to Selina. So it's all there. He's a master and he's also rich so he has connections. The only problem was that i understand how people wanted to see him actually get in. That was a running-time problem. I would have loved to have seen Bruce take out some people or at least a shot of walking the ice again like in Begins, but this time that ice is Gotham. Would have made for a damn good parallel shot. But the end of MOS? Perfect ending, but it doesnt make any sense seeing the Daily Planet stuff and the high spirits of everyone as if nothing happened. That's bad writing from Goyer even though the individual scene is executed well by both Snyder and Zimmer.