I've seen some horribly rusty 1st gens, but no rusty 2nd gens. Material or design in that area is better. Not something you face on the wet coast!
Also there seem to be more battery failures in the 1st gens.
And -- NERD ALERT -- better EPA ratings! Gen 1: 41 mpg US combined vs. 46 mpg for gen. 2 (50 for 3rd).
Also, there just aren't that many around here. All that said, I'd probably get a 1st gen if the price was right and it wasn't swiss cheese.