Maybe I played a different SS2 but the one I played didn't have any choices in it at all, besides the class selection at the start. In fact, I'd even go as far as to say that BioShock has more choices (actually one, but SS2 has zero) with either harvesting or rescuing the Little Sisters that influences the ending.
And what do you mean exactly with character development? Obviously not Goggles or Jack, because at face value they're as thin as paper (with Jack actually having a lot of subtle lore about him), but both Von Braun and Rapture had a lot of logs you could find that gave plenty of depth to the characters in them. In that regard I'd say they're equal.
In terms of holding hands, I agree that the default pointer in BioShock is cancerous, but luckily you could disable it completely and still navigate around very well with the environmental feedbacks. So taking that into account I don't think they're very different in that regard. Still, because of the default pointer, SS2 wins here.
Besides mechanics (RPG/FPS hybrid, pure-ish FPS) and setting (space, steampunk), I'd say both are almost identical. It's hard to love the one and hate the other, they're too similar for that. Especially in terms of story telling and mission design it's hard to not see a lot of similarities.