My questions (WITH SPOILERS):
1) How does Batman survive the fusion bomb at the end? He was shown to be in the cockpit of his plane mere seconds before detonation, and the blast radius was at least 6 miles. They said "autopilot", but I didn't see him eject in time. Also, he would then land in the icy water, in full body-armor, and either sink like a rock or freeze to death in minutes. Plus, if he swam to shore, someone would've spotted him.
2) How did Batman get INTO Gotham in the first place? He was stripped of all his gear and belongings and Gotham was entirely cut off from the rest of the world. How'd he get into the city?
3) The giant, flaming bat-signal on the bridge. Yeah, it's cool and all, but when did Bruce get the time to climb the bridge (monitored by both police and criminals) and prep it with gasoline all over... and then calmly wait at the bottom for Gordon's execution to spring the signal?
4) If the goal of the League of Shadows with Ra's Al Ghul was to eliminate the problems of Gotham by destroying the city, and 8 years later Gotham is practically crime-free, citizens are living peacefully, and Batman himself is retired, why on earth would they attack? Gotham HAD peace. They're the ones that caused all the problems.
5) If the true aim of the League, Talia, and Bane was to dupe Bruce into giving them the bomb, why did they jeopardize their plan by staging massive terrorist attacks that served no real purpose other than to get their men killed and put their plan at risk?
6) How did they know where Batman's armory was? The only ones that knew were both Bruce and Lucius Fox.
7) Batman's plane seriously was just camped out at the top of a building for nearly a year? He didn't even take it back to the cave. He just left it out in the open under a suspicious looking tarp and nobody found it?
8) It may not be a plothole, but does the movie seriously expect me to think that a 10 year old girl has the strength and will to crawl out of a hole in the ground, but none of these strong, full-grown men could do it? Or, for that matter, they couldn't just build a ladder or something out?
9) People know who Bruce Wayne is. He's a rich, famous billionaire playboy. If Bill Gates faked his death and was then spotted in public, you'd think someone would notice.
10) "You won't give up on me, will you Alfred?" "Never." -Batman Begins. Alfred totally gives up on him. Dammit, Alfred!