My biggest qualm with the game is that it's TOO SHORT! Still, I'd much rather a game feel too short and make you wanting more than have it feel like an eternity to get past plotpoint X.
As for online activation, I bought it through direct2drive.com which already has a similar system on all their titles. It's not too much of a hassle to get the license reinstated for your game, just takes 24 hours of downtime though, and as Stephen said, it sucks when your internet's down for the day.
I got the Orange Box collection through Steam, and that whole "you must be online 24/7 to play our single player game" thing got pretty old. Usually my singleplayer games are specifically to be played when the cable goes out.
I think the best part of Bioshock is that Quark (Armin Shimmerman) does such a phenomenal job in his voiceovers as Andrew Ryan. His main intro monologue for that game is among the best in the business.
YouTube - Bioshock Intro & City entry