Things missing in SR3 that were in SR2:
Secondary hair colors
Clothing layers <-- this is huge for me
socks <-- lol
walk animations <-- could be a hit if you care enough
The character customization itself has been downgrade just a tiny bit in regards to the minute details, but the clothing options make up for it. I was picky in regards to clothing in both 1 and 2, but I love every piece of clothing in Third's Initiation Station and this isn't even the full clothing palette. Also, the Third's character creator allows you to go far and beyond. SR2's character creator, unless you're playing on pc, is mostly surrounded around human characters. In SR3, you can make whatever: superhero, robot, Dr Manhattan, zombie, alien, and the game actively gives you the tools to do this from the outset.
So in many ways it's a huge upgrade from 2, but it's also missing some of the more intimate details that made 2's great (clothing layers for example). I see a lot of suit jackets, and most of them come with pre-fixed turtle necks and shit. In SR2, if I wanted, I could put on the jacket, then a t-shirt of my choosing. Not possible in SR3.
