I don't know, The Behemoth (Alien Hominid - not that those graphics are hand-pixelled, exactly, but close enough) seem to have done pretty well and are set to release another game eventually. Cave and Treasure are both rather small companies, as well. The Nippon Ichi games seem to have a pretty good following too. Darwinia for the PC (3d graphics, small company) also got some excellent reviews on mainstream sites recently.
I think both small developers and 2d graphics have a place in gaming's future- the developers because well-designed gameplay will always be sought after by some people, and the graphics because for certain genres like fighting or shooting they're just the best way of presenting the game.
I think both small developers and 2d graphics have a place in gaming's future- the developers because well-designed gameplay will always be sought after by some people, and the graphics because for certain genres like fighting or shooting they're just the best way of presenting the game.