My recommendation is for a sci-fi version of battlelore.

Battlelore gave the Warhammer Fantasy Battles feel on a smaller scale.

Why not do the same with a smaller scale version of Warhammer 40k? I know GW tried to do this with Epic and failed miserably, but it seems the Battlelore system works better. Apparently if you simplify the rules and add a board into the mix, popularity ensues.