Most certainly System Shock 3 - a good old single player emergent FPS with a lot of scariness and a focus on "oh crap, there's something breathing raggedly outside of my makeshift hiding space and all I have is a 2x4 and this audio log" and not "ah, here I am with my powered-up rocket launcher, take that aliens!" type of atmosphere.
I'd like a healthy, beefy dose of Fallout 3; non-molested and innocent of MMO conventions and deathmatch multiplayer nonsense. A gritty, gory, dirty single player tale of love and loss in the wastleland.
Master of Magic 2, for God's sakes! Where's the humanity!?
A non-console-trashed sequel to Deus Ex.
More stuff in The Guardian Legend , Kid Icarus, and Blaster Master mythos.
A sequel to Shin Megami Tensei: Nocturne that expands and develops the demon fusing, fiend fights, and overall artistic direction from that title.
For original stuff... I want to be a tidal pool organism (randomly selected at the start of the game.. you might be a sea urchin, a sea star, a crab, a fish, a sand flea... etc... ) that has to journey from tide pool to tide pool , slowly discover the world outside of my sandy resting place and the terrible tragedy that unfolds on my little beach.... yeeeeaa!