This is a massive thread so I didn't read it all, so I apologize if my thoughts echo ones previously mentioned.
I am of the opinion a person can like or dislike whatever they want. Opinions are opinions and everybody has the right to theirs.
BUT....I do think opinions can be ill informed and reactionary. Does that mean all the opinions I vehemently disagree with are reactionary? No, but I can't help but feel in this case, much of it is.
No one, not a single person can honestly say with a straight face that TDKR has any more plot inconsistencies or "holes" than TDK. I've seen fans completely dismiss points brought up against TDK in defense of Rises simply because "IT'S TDK ZOMG JOKER NOLAN TWO-FACE IT'S PERFECT END OF STORY!"
They can refute any point you make agaisnt TDK, but when you do the same thing to Rises, you're just a fanboy apologist. The simple fact is you can nitpick TDK as much, if not more than Rises.
-What was up with the school buses in the beginning? You are to assume the Joker planned all of those buses to be there so he could blend into them. But you hear childrens laughing, indicating that these are regualr school buses, in the soundtrack. Did he know these buses would be there at that exact moment? What if they were late? What if there was a traffic jam? None of the drivers noticed a freaking bus pull out of the wreckage of a bank? No one reported it?
-What about the whole skyhook thing? Bruce is seen jumping off of his yacht to a suspicious plane run by foreign smugglers. Later on, we are to assume these same smugglers are the people to snatch Bats up with skyhook in Hong Kong. For one, how did these guys not put two and two together? How did they not know it was Bruce they picked up from the yacht? Did Bruce use a false name? Was he not recognizable? How did they not say..."hey this guy is Batman we just picked up, I wonder if it's that rich dude we picked up a few day ago? You think they're the same guy? Does Batman work for him?" And how did that freakin' plane manage to fly over Hong Kong airspace without detection or without being forcibly redirected?
-Where did the Joker go after he threw Rachel out of the window? Ya, ya we know there is a deleted scene showing what happens, but it's not in the film, nor is it even available on the DVD. So that's not a good excuse. He came with the purpose of finding Harvey. Why did he just give up?
-How about the Jokers plans requiring him to be, literally, omnipotent? There is no getting around the fact that Jokers schemes crumble under a little thinking about the logistics. It is literally impossible for him to concoct all of these plans by the seat of his pants so fast one after the other. He is a "dog chasing cars" as he puts it. A guy who just "does things". The assassination attempt for example. The city has gone to hell, the mayors life has been threatened, but nobody notices that the Honor Guard is a set of totally different people? Nobody notices the SCARS on one of the dudes face?
-What about the "fire truck" gag? There is a fire truck on fire in the middle of the city and nobody calls it in? Where was everybody anyway? Gotham must be the most boring city to live in, the streets were deserted. The cops even fall for the fire truck gag! There was no context to the set up. It was just a random fire truck on fire, in the middle of road. No other emergency vehicles present, no firemen, no FIRE anywhere in site. You would figure the criminal who has been 10 steps ahead of you the whole time would try to divert you would you?
-Did the Joker know Batman would save Harvey in the nick of time when he shot the bazooka at Harveys truck? Joker needs Harvey for his plot. He is the linchpin of the whole damn thing! Why shoot a BAZOOKA at his truck?
-His whole point was corrupting Harvey Dent right? Why set up the chance to kill him in the explosion? Did he know Bats would be the one to save him in time? Did he have another plan set up if Harvey just exploded right then and there? What would become of his plan to corrupt him then?
-And how did Joker know that cop would stay with him, alone, in the interrogation room giving him the chance to escape so he could set off the bomb? Why would the cops be that dumb as to leave one cop alone with the Joker, who is un-restrained? We don't even see The Joker get the better of the cop.
-How did the Joker and his henchmen rig up the hospital and ferries with explosives? A hospital is run 24/7 with staff. How did no one find the bombs? Stumble onto the goons planting them? Same with the ferries. How could nobody find a bunch of explosives on a public transportation unit like a ferry? Gotham doesn't inspect their stuff?
-How come Harvey wasn't the first person to be evacuated? Where was his security? Arguably the most important man in the city right now just escaped a murder attempt with half of his face disfigured, and you don't have a few cops posted about to keep an eye out? A guy with a painted face can just waltz in to his room with a nurse outfit and gab with him for 10 minutes and nobody comes in to get him out?
But no, all of this is forgiven and brushed under the rug because, ITS THE DARK KNIGHT! But Batman getting into Gotham, or the logistics of the plane crash, or the quality of the cops freshness of the cops in the sewers are somehow more unforgivable than anything mentioned above.