I don't think the violence in TR, Bioshock or TLoU was too intense (well, Lara could have done with a few less spikes through the head); I think the problem is that it's ceaseless. You continually kill logistically impossible numbers of people. It leaps over the ridiculous and lands into the implausible, as repetition turns a life-or-death struggle into an obstacle course.
Rote combat gameplay could probably make some point about violence, but I can't imagine it would be easy (and I've only ever seen Spec Ops try to do it). For most action games, ceaseless violence seems to be the objective - if it's fun, original, challenging and well-balanced, the game shines even if the story is an afterthought. But when action games become heavily character- and narrative-driven (as many recent action titles have been), much like RPGs, then players start to demand that the themes and conventions of the narrative be reflected in the gameplay. And ceaseless combat cannot do that. It's like playing Beethoven's 5th on just a cowbell.
RPGs deal with this in several ways. Combat may occur inside a bubble-verse, with entirely different (often abstract) mechanics and presentation from the rest of the game. Tactical or turn-based mechanics make even a small enemy group take a lot longer than shooting a terrorist in an FPS. There are often several ways of interacting with the world (Suikoden II had three combat systems--party turn-based, strategic army clashes, and personal duels--and a heap of other activities like investigation, castle renovation, gardening, dancing lessons, dramatic martial-arts cooking duels...), and several layers on which the world can be explored. Even in the most seamless RPGs like Bethesda's, there's often a "click" when the world switches gears from interaction to combat.
I'm not saying modern action games need several other mechanics in addition to combat. I like ceaseless-violence-obstacle-courses. But they are being stretched at the seams by narrative-driven games, because their core mechanics simply lack the range to transmit all the nuances of a well-crafted story. The game ends up looking like it's ignoring the narrative or distracting you from it, which is what most of the Bioshock-griping was about - wanting to spend more time with the characters and the general population, and not in obviously limited combat arenas.