I really don't want to admit this to myself, but I think I like Saints Row 2 better. Not heaps better, just a little better. There are things which SR3 does better than its predecessor... well, a lot of things, actually.
I think I just changed my mind over the course of writing that sentence. The only thing SR2 does better are cutscenes (they are rife), and layered clothing -- though that clothing is less attractive by far than the offerings available in SR3.
Alzo: There are less busywork missions (no Strongholds). The money actually makes a difference and is still largely in demand even though I'm 16 hours into the game now. The game is very good looking; somehow they managed to hold onto the sort of stale urban design theme with wacky facades which makes Saints Row what it is, but the lighting, L.O.D. shifting, and environmental elements they've added make this the first game.
The only thing I can complain about is that the city is larger, and less explicitly landmark-friendly. It feels like there are several docks, several factory areas, and several suburbs -- but I couldn't tell you, because whenever I open the map, I'm always surprised to find out I had NO idea where I was on the overall geography.