If allies come back, they should work exactly like they do in Fantasy. (ie: they're for multi-player games and/or 'opponents permission' type games and most definately NOT! for mainstream play!)
Allies coming back, especially into any kind of a competitive setting will just screw up the entire edition and turn it into a giant mess of OTT stupidity. Doesn't matter how you try and restrict it, all allies will do is allow armies to ignore their buint-in weaknesses and the game will suck rotten monkey-balls.
Imagine for example a GK paladin army, now backed-up by blobsquads of IG?!
Or how about CSM's summoning in bloodcrushers + plaguebearers?!
God forbid you run into Eldar teaming up with their dark cousins! (fotuned venoms & doomed squads getting hit by wyches should be real fun, right?!)
I'd hate to be the poor bastard getting to fight hordes of Ork boyz backed-up by Plague Marines & Oblits...
Allies just break the game. Leave them to multi-player & special senarios, or else risk destroying the entire game for the next 4-5+ years!
I agree, I really hope if there are allies rules that they are for multiplayer. Also I'm hoping that it would be more than order vs. chaos since 40k seems to have more teams then that.