First of all, Metroid's "Stagnant" environments, as you called them (which are anything but) create a sense of isolation and mystery. As for stagnant.....have you ever even played Metroid Prime? The entire world feels like it's a living, breathing environment thanks to superb ambient sounds, organic structuring, creatures that go about their business even when you're not around, and absolute top-notch artistic direction. Bioshock does little to bring real life to it's world. There are ambiant sounds, and the occasional splicer talking to itself or whatever, but the whole place feels dead, lifeless. I'm aware that it's supposed to be the game's motif, but there are ways of creating that mood that don't make the environments feel lifeless.
As for shooters lacking depth, when it comes down to it, they really revolve around 1 simple mechanic: Shooting. A shooter has to have shooting as it's main focus of gameplay, otherwise it's not considered a shooter, and when you're gameplay revolves around one simple, repetitive mechanic, it gets stale very quickly. Certain other games have extensive amounts of shooting, but because they also have other major gameplay elements, they aren't considered shooters, and become something much more (again, Metroid Prime works as a fair example here, though it is much more adventure-heavy). My point is, it doesn't matter if you can take cover, or drive vehicles around or whatever, IMO, shooters are still a stale genre in desperate need of an evolution that will turn them into something more than just a shooter.
Anyway that's my 2 cents
