Plot Holes for TDKR 

Bane's Overly Complicated 5-Month Plan - Assuming this is categorised as a "gripe" not a "plot-hole"... Either way, kinda irrelevant because Bane and Talia explain why the plan was what it was.

Bruce Wayne and Miranda Tate's Out of Nowhere Hookup - Isn't "out of nowhere" in the context of Bruce's character at that point in the film (as this article even points out), and certainly isn't out of nowhere when we are told who Miranda really is.

Terrible Hand-to-Hand Fight Action That Makes No Damn Sense - That's an action movie convention. Anyone who has ever watched an action movie knows that any and all minor characters can be killed with a simple karate chop while the main characters are way stronger and will inevitably have a brutal battle or two. 'Kick-Ass' is the perfect example of this (ie Hit Girl takes down all the massive, gun-toting trained killers, but then quickly gets beaten by a skinny guy who has sat behind a desk for the entire movie).
"he doesn't employ strategy or gadgetry to defeat his stronger nemesis" - Uh, yeah, because he tried that and Bane laughed in his face. The whole point was that Batman had been down in the pit too (literally and figuratively) and that he was then capable of besting Bane in a fist fight because he felt the same rage/despair/hope/anger/love that Bane felt, but because he's the good guy with more pure motives, his strength wins out.
But the Catwoman killing Bane thing drives me nuts too. He deserved a much grander death and Catwoman deserved nothing. I think if the movie had been split into two movies. Yeah, like 'Harry Potter,' I know its lame, but I think the problems with TDKR would have been solved with even more time, but split time.

Batman's Superhuman Time Management - I choose to believe he's dead in the end, so there aren't any problems with that interpretation. As Alfred said early in the movie, Bruce had a death wish.

Bruce/Batman's Coincidental Death - Yeah, but in every Batman movie ever, it has been very obvious that Bruce Wayne is Batman. Its part of the Bat-verse in-joke.

Bruce and Selina's European Vacation - Like I said before, I don't think Bruce is alive. I interpret that scene as an hallucination/fantasy/dream/alternate reality.

Selina's Special Friend, Wink Wink - I have a whole grand theory on this, but I can't be bothered going into it. I think it fits into the story just fine if you read Selina Kyle/Catwoman in a certain way.

Good luck, Robin! - There is obviously a plan there. I don't know what it is, but there is one.

Room For The Justice League? - I hope not. It doesn't need to follow the lead of Marvel franchises. Batman characters are always better on their own anyway.

Even if you choose to believe he's dead, it still doesn't explain how he did the things he did before he died.

Btw, I admire how much thought you've given to it.

Thanks! Kinda obsessed with it right now!

If he, like Alfred suggested, had a 'death-wish,' its likely that he went into the last battle with Bane expecting that he would probably have to die, so he could have organised that stuff at any point before that. Thats just how I explain it all anyway.

Well, death wish or wish of faking his death, he would surely want to arrange all that in both cases. Question is, how? And more importantly, when? Even if I accept that he had his legal affairs sorted out a long time ago, still he could NOT have had to do everything from the bag for Blake to the gasoline bat signal

Unless he organised those things even earlier. The bag for Blake, for example, could have been organised much earlier on, like quite soon after Bruce met Blake. But I agree that the flaming Bat signal is obviously illogical time wise and is used a symbolic flourish from a cinematic perspective to represent hope for the Gotham people. I guess its one of those things Nolan would want the audience to forgive because what it symbolised was more important than the logistics of it.

Let's say I forgive the gasoline signal.

Even while I was watching the movie, some things bothered me but I ignored them. Like Batman's superhuman healing or getting back to Gotham. (As a comic book fan, it's ridiculous to even ask how BATMAN got into Gotham. It's his freaking town, for crying out loud. In the movie, secret service guys did it too).

Even then, some of the questions raised in the article look pretty valid to me.

Long story short, The Dark Knight had no major plot holes (if you overlook some aspects of The Joker's plan of getting caught.) Inception had none whatsoever, for me. Then there are Nolan movies like Memento and Prestige written with such astonishing brilliance that made me worship Nolan. It's he who set the bar so freaking high.

So when I saw so many illogical things in TDKR, it was kind of a letdown. (The day turning to night during the Stock Exchange chase, what's up with that?)

However, I still LOVED the movie.

True, there are a lot plot holes in TDKR, compared to other Nolan movies. And I think that comes from the movie having so much going on in it that it really could have been divided into two movies so that those plot holes are filled in.

I guess for me, they are plot holes that I can fill in myself. I've read a lot of reviews that have raised the same or similar issue about the movie but still conclude that it is a great movie, so I think that Nolan either wants us to forgive the holes and appreciate the totality of the movie (and Batman's character), or he wants us to fill in the holes ourselves. Maybe its a little bit of both.