Basically Dwarf Fortress, but sci-fi, with space travel and with really good 3D graphics.
An overly complicated simulation of an entire universe where I can do anything that the game's laws of physics allow me to do. Particularly, I dream of a game where you can fulfil Star Trek fantasies of solving convoluted problems with equally convoluted solutions; but without it being a pre-programmed option. ("Reconfigure the deflector dish to output a neutrino wave to counter act the tachyon field!")
Fake physics that allow for real fake science and engineering.