I'd like to see Dark Heresy done Infinity Engine style, so maybe let Obsidian have a crack at it, looking at their Project Eternity game. BG2 had Wild Magic, so there's your Perils of the Warp straight away!
+1 for XCOM 40k I'd also love to see some type of chapter management game. Think the second poster mentioned it. Not quite a sim, but any type of game that lets you either play or sim battles then allocate men and resources to neighboring systems, manage promotions, etc.
The most likely candidate I see is a Civ stile game. A small indie company can produce a game like that based directly on the table top but large scale and the only thing they have to figure out and test is UI and Animations. As we saw on Space Hulk. Being a computer version of a table top game is fine as long as the production is solid. Unlike what Space Hulk has.
One thing i always dreamed about was the tabletop as a pc game. From setting up your army to colouring it, from measuring distances to rolling dice for hits and saving rolls. that would be my dream. I am pretty sure thought that it will never happen because if there would be the tabletop as a pc game GW probably would make way less money on miniatures. So it will always stay a dream unfortunately.
