If only the 9900 had the battery life of the 9000, I'd say 9900 hands down. I wouldn't mind if the 9900 was the same size as the 9000, that's just me. [As far as the thickness and all that goes.]
The 9000 was my very first BlackBerry ever, and I haven't looked back. Went from that to the 9700, then 9780, and now I'm rocking the 9900, with that being said I'm satisfied with how it caters to my needs.