For me the biggest flaw with the first game was that they made too many concessions to make it like other mainstream games and took away a lot of the feel that System Shock 2 had. I think it was a really good game, with a fantastically original setting and story, but it definitely seemed like they did everything possible to idiot proof it and it really was hurt by it.

I'd like to see what they do with the story in the sequel, but if there's nothing really new to Rapture then I'm not sure how interested I'd be in re-visiting.