They very well could. But I didn't like
Bioshock 2 all that much, so my hopes aren't high.
Continuing in the Fallout 3 vein, resistance to its development came in two camps, primarily - one, that Bethsoft didn't have the writing prowess to correctly pull off the Fallout setting, and two, that the change from turn-based isometric gameplay to real-time FPS gameplay would result in a far different and inferior game. Aside from a few minor things, I think the first camp was proven wrong. Camp two was half-right, in that F3 was very different from its forebears, but it was different to such an extent that outside of editorial opinion there wasn't much use in debating if it was better or worse, as a game.
Anyway, the thing about Fallout was that it was a role-playing game first and a turn-based combat game second. It wasn't a particularly deep or effective turn-based combat game in any way (in the first Fallout especially, many of the combat skills are comparatively useless, and the companions are famously unreliable in any role except "bullet sponge"). Aside from aesthetic considerations the transition didn't hurt that much. The game's core attributes - character creation, skills, dialogue, narrative design, the RPG part of "turn-based RPG" - didn't change drastically. X-Com on the other hand didn't have that dual nature. It was a turn-based strategic combat game, and that's all it was. Changing the nature of combat changes the core experience of the game. XCOM will be different from X-COM and sheltered from comparison in the same way Fallout 3 was, but the question of whether or not it makes sense to say they are of a kind except in the most superficial way will remain open. Whether or not that question is worth asking is yet another question.
Really the big thing is that there has yet to be a single TPS / FPS with squad control that is any good at all.
Ghost Recon: Advanced Warfighter 2 had pretty great squad controls.
I remember playing the first game but all I remember is it being very different from past Tom Clancy games. I don't remember the squad combat being
bad, but then I think I probably played it like an FPS, doing most of the stuff myself. Probably explains why it was so hard.
Anyway yeah, among other elements the thing with turn-based (or even just real-time isometric) gameplay is that it affords a much greater amount of control over the whole squad. Even with complex squad commands you're still relying heavily on AI in an FPS / TPS (barring a Space Hulk-y "body hop" mechanic, which is even more antiquated than TBG) and that is problematic in the most optimistic estimates. Advanced maneuvers that are simple in turn-based play like flanking are a lot harder to pull off.