Despite being in production for a long time, and despite Nolan's supposedly great editing skills, the final film was a messy, inferior version of what it could have been, with unresolved plot strands (no matter how insignificant), and half-developed features that had no place in a film of this scope or this scale. Especially not one that was supposed to offer finality to a series.
Instead of the appropriate full stop on the trilogy, The Dark Knight Rises was full of hows and whys: how did Batman get back to Gotham and why did he waste time on creating some street art when he returned? How did Blake recognise Batman from a smile when no-one else has ever managed it? What kind of magical drugs did Bruce Wayne take to fix both a knee that needed bracing and a back that was broken in a few short months to the extent that he was superior in strength and power? And where can I get some?
How To Fix It
Just generally write a tighter script: unfortunately for Nolan, the trend from Batman Begins through to The Dark Knight Rises was of decreasing writing quality, despite the increase in hype, and the amount of errors in the third film compared to the first was just embarrassing.
The problem for Nolan was the issue of multiple balls in the air: faced with unprecedented hype and the considerable challenge of making something of the necessary scale to end the biggest comic book trilogy of all time the director tried too much, and ended up losing a grip of some story elements. Though the temptation for the next Batman film will almost certainly be to go grand again (albeit via yet another reboot) the next director would be a lot better served focusing on a tighter vision for the character.
A lot of the biggest plot-holes could in fact have easily been hidden, had the next point on this list been more strictly adhered to...