If they'd have made the new X-Com game to run as a FPS, all manner of hellfire and brimstone would have been rained down on them, same case here.
There are some things that go outside of 'storyline' when defining computer games, it's like serving pasta on a bed of jam, they might both be delicious individually and appeal to Pasta Lovers in one case and Jam Lovers in the other, but try and put the two together and you get something that appeals to neither, even if they like both individually.
It's the fact that a lot of companies view the computer game industry like the film industry, Computer Games have several 'methods' of delivering the story in the way you interact with the interface. Games like Syndicate Wars worked because you took the role of the 'unseen controller', usually the character in the movie who appears only for the final scene, if at all. Computer Games are the only media where the Protagonist can actually be completely invisible throughout the experience. FPS Games, however, are the complete opposite, making the Protagonist the central interactive focus of the game, where you quite literally control his/her every action.
There's nothing wrong with that, it provides a more intense, personal experience, but in the case of Syndicate Wars, that's not what made the game so great, quite the opposite in fact, it was the removed, 'distant' style of gameplay that made it work.