to be honest , i think the best engine i've see which would be cool to see a FPS version of W40K would be the world war II online one, last i looked at it, it wasn't graphicly as advanced as the current likes of Cod4 but it has 1 hugh map with every one plays on, so it would have multipal battle fronts, the system allows for commands and brigades and the same sort of hierachy(spelling) that would benefit a w40k online fps.
The vehicles (tanks, fighters and bomber planes, ships, AA guns, AT guns and the such) run off locational damage model, also have crew postions (aka driver, gunner, loader, comander), so for a example, if you manage to get a sapper charge placed on a tank near were the fuel tanks are and that vehicles armour was rated to be in rl to have XX amount of mm thick you could kill it in 1 hit, but then on the flip side you place a charge or shoot it with an AT gun say on the heaviest armour part (say the front) your shot may not even effect the vehicle, So it draws even more tactics in when tactle a vehicle, also you learn were the vehicles "sweet spot" is if it has one
also you can also kill the the different crew positions, so if your driver is dead and no one else got hurt, you lose control of the vehicle (if you were stoodstill at the time you can't move, if moving you could well be carrying on in that direction) but you cna still use a turret and such if your in a tank.
its one of them games were its a really steep learning curve, but if you get into all the squad (guild/corp) thing it is really good on the comraidship side, also there is the high command sides if you fancy taking control of a campaign (which can run over many weeks) and control were brigades (which are made up of the different player squads) but all that is generally run through the games community.
there's some much more i can't explain which would make it a very good contender for a w40k fps