I've been seriously thinking about how I'd go about making a modern Quake-like for the past year or so, and as you guys touch upon; Metroid Prime and Dark Souls are absolutely games to look for inspiration from.
One thing I think that would be a really good thing to borrow for consoles, is the Metroid lock-on mechanism. When you lock on to an enemy, you enter circlestrafe mode, where jumping allows you to do a quick dodge move. Coupling that with some spatial awareness to try to prevent unintended falls off edges, I think that would go a long way towards a more Quake-style combat feel.
For PC mouse and keyboard would of course be the preferred way.
The meat and bones of a modern Quake would be the monsters and the world though, so that's where most of the effort would have to be focused in my opinion. :)
I can't even count the number of different
weird-ass monsters in Dark Souls, so it is always so disappointing when I see a game that only features Men With Hitscan Weapons.