I think the difference between the two movies is that Obadiah Stane was a much more compelling villian. It's not that Rourkes' Whiplash was bad by any means, but his motivations in the movie were not as interesting as Obadiahs. In the end, he was just another bad guy looking for revenge against the hero. It can be argued that Justin Hammer wasn't really a villain in Iron Man 2.
I disagree with those saying the movie on Tony Stark's end wasn't interesting or having depth. I thought he owned every scene he was in and his story arc was interesting.
Things that I personally would have changed would have been....
-No Black Widow. If they were going to stick with her, they should never have revealed her identity at the donut shop. That was truly pointless and overlooked by most in regards to this scene. The Fury/Stark stuff was brilliant and funny in my opinon. She kind of had no point in that scene.
-A longer fight scene on the racetrack. That scene and build-up was incredible, but the fight was a bit underwhelming once Tony got the suit on.
-Longer final fight with Whiplash, whose armor should have been red and more interesting. Also, it should have been IM vs. Whiplash, not a tag team match. Keep the WM/IM team up against the drones. Also, the 'crossing the streams' angle was used twice in the movie and the finishing blow to Whiplash should have been more original. Again, it was a great scene, but just a bit too short and sweet. The actual fight was one of the best superhero fights put to film.
-Axe the airplane scene with Pepper and Tony. This is the one scene that I thought was boring and out of place with the rest of the movie.
-More Rhodey/Stark and Stark/Whiplash scenes and less Whiplash/Hammer.
Aside from this minor grievances, the movie was wonderful. I can't let these minor things really ruin any movie for me. The good parts of IM2 make up for the lesser parts. Pretty much every scene up until after Stark meets Whiplash in jail was perfect. Same goes with every scene after the Stark/Rhodey fight (which was still entertaining IMO).