There's a huge difference between Bane and Ultron, in that Bane was every bit as threatening as the trailers made him out to be. You got the sense that his own men both feared and revered him, they're willing to die for him (him, not Talia). He was cold and exacting in his methods and he inflicts real damage to Bruce and Gotham. Best of all there's an actual humanity beneath the monstrosity, it's just been severely twisted and warped. Some just can't seem to get over the character's last 5 minutes in the movie, but that's a whole 'nother discussion, because he wasn't just a lapdog. I could go on but that's beside the point. AoU didn't even come close to scratching the surface of how menacing and dangerous Ultron could've been. He was entertaining, but not really that memorable and dare I say iconic, in his own offbeat way. Bane, love or hate the voice, was very memorable. This is just another example of DC simply outclassing Marvel when it comes to crafting great villains.
I really still feel that from a filmmaking and writing perspective Rises is actually pretty strong and severely underrated. The themes are woven in with a degree of sophistication across the various character arcs in the film, it feels like a natural culmination of the series, it has a sense of both timelessness and urgency in the social issues it touches on (doesn't get much older than the poor vs the rich) while never gets bogged down in making it a political movie ABOUT the 99% vs 1%, but most importantly there's a strong emotional throughline that carries through the whole movie. I think it's actually kind of amazing that while Rises may be the most 'clunky' of the trilogy in terms of having to cut some corners through its epic plot to get it into an under-3 hour film, it somehow manages to be the most emotionally resonant in spite of that. That's because the heart of the film is the Bruce Wayne arc and that is handled absolutely perfectly IMO.
With Ultron, I don't even know what the heart of the movie is. Hawkeye I guess? Or maybe Black Widow/Hulk's love story? Who learns what in the movie? Where are the character arcs? It's a very entertaining ride, but it just feels like nothing too important happened the more I reflect on it. Like a filler episode of a TV show. I'm not trying to take a dump on the movie, I actually enjoyed it more than the first one, but if you want to talk putting on your film nerd hat...for me TDKR is definitely more than a cut above it in that context. Avengers definitely feels like Joss Whedon struggling to make a movie amidst working in the Marvel machine and studio interference. TDKR feels like the Nolans and Goyer struggling a bit to live up to TDK, but ultimately still crafting a worthy conclusion that solidifies the trilogy as a single body of work. I would have to agree with jmc that it's a testament to the talents of both Whedon and Nolan that they were able to prevail to varying degrees (depending on your opinion of the movies) in spite of the mammoth tasks at hand.