I just saw TDKR yesterday, and loved it. However, I still think TDK is the better film. TDK felt more focused and cohesive; especially the second half. Story wise, TDK hits a bit harder as well because it's so devastating personally for Bruce Wayne, and ends with him basically giving up. While TDKR has plenty of great action set pieces, it doesn't come close to topping the armored truck sequence from TDK.
I still can't decide whether the Joker or Bane was the better villain, though. Ledger and Hardy both delivered excellent performances. The Joker was manic, psychotic, and didn't have any clear motives. Bane was just plain intimidating.