Well, this would be a large scale scenario, but since we're talking about 500 v 500 player battles, it might work: I was thinking of a multi-tiered battle system, maybe starting with ships in low orbit, trying to take out each other's air defenses. Once one side has won, the battle would go to the ground, with the opportunity to spawn back up at the ships still an option, allowing you to take a drop pod or whatever as a transport, maybe launch a flyer, or do some other things you generally wouldn't be able to do on the ground.
The addition of space battles will create more stratigic as commanders or players will have to balance their forces equally to avoid losing either battle. Space battles are too important to the warhammer 40000 both game wise and fluff wise, the heresy started with cruisers firing bombardments at loyalists on istavaan III.
maybez we'z cud invade anotha clanz krooza? And den you';z have to fight us off! AND IF YA LOSE WE TAKE YER 'EADZ AND YER GEAR! uehaaa iz' excited now boyz! WAAAAAAAAGHHHH!!