Doom 3 – you know it. Peoples complained about predictability, and too much darkness, and teleports. Darkness was relieved with embedded flashlight later. Never played the game.
Alone in the dark 4 – it still puzzle/horror in style of Resident Evil (i.e. less for horror and puzzles, more for kills).
Arcanum of ...– good RPG in vein (and from authors) of Fallout and Fallout: New Vegas.
Battle system is quite cripples, but it more than covers it with quest system, vast world and tons of interactions.
Planescape Torment – the best realization of pen-and-paper RPG that I know. Lot of text, lot of choices, occasional combats and totally unusual protagonist and plot in whole. My choice... but I am exactly in _this_ field of games.
Might and Magic 9 – it's not exactly M&M in terms of universe, diversity and plot. Still can be enjoyable, I suppose.
Legacy of Kain Soul Reaver – metroidvania with extensive plot. I.e., gameplay is "explore level, gain a lot of knowledge by the way, find the boss, kill him and receive new cool ability that will allow you to enter next zone and also found several secrets at the old ones".
Choose yourself!
P.S. Did you try System Shock? It's semi-shooter/semi-puzzle/RPG at the space station with huge levels and several puzzles. Can be tuned to be less puzzled (or less action) or go just opposite. Highly recommended.