Is this thread about roguelikes with 2D world and 3D graphics, or roguelikes with 2.5 or 3D world and 2D graphics, or 3D world and 3D graphics like SoulFU? :)
IMHO SoulFu isn't a roguelike, it's in realtime and it's very graphical. Roguelikes should work with or without graphics! :) I also found SoulFu to be completely unplayable without a joypad so I didn't get very far :( Very nice graphics, though.
For a 2D world and 3D graphics, I think the Dungeon Master style of first-person pseudo-3D could work well, but would need at least an 8-way view instead of a 4-way view so that the player could see things diagonally from their position. Turning should probably take zero time as well, to avoid disadvantaging the player for using this view instead of a standard top-down view.
For a 2.5 or 3D world and 2D graphics, how about "look up" and "look down" controls that raise or lower the view plane on the y axis? To make it less tedious to constantly scroll the view up and down, you could also try to show the next highest thing above the current view level if there is only solid wall at the current level, and the next lower thing below the current view level if there is only empty space at the current level, if that makes any sense. To make it less confusing, colours should be used too - e.g. anything above the current view plane shown in yellow, and anything below in blue. So if the tile next to the player's position is blue, then they know there is a drop there, and if it is yellow, they know they have to jump or climb to get there.
I'd try and construct an example of what I mean, but it's damn difficult without being able to use fixed-width text and colours at the same time :/
Here's an example of the monochrome version, which only shows the level you're currently looking at to avoid confusion. The example is a room with 3 overlapping levels. On the middle level (where the player is) there is a pit on the eastern side of the room and an alcove underneath the raised section to the south:
View at current level:
##########
#........#
#...@.. #
#...... #
#........#
####..####
#..#
####
View at one level down:
########
@ #......#
#......#
########
View at one level up:
##########
# #
# @ #
# #
# #
#........#
#........#
#........#
#........#
##########