I have always played "every man for themselves" in the past, and that was what I originally envisioned, but I see a lot of wisdom in the grouped factions the more that I think of it, and hear from others. Assuming we do go with grouped factions though (nothing is written in stone yet), the issue I see is that on the one hand thematically/fluff wise you really need at least 3 factions to make sense. Say something like:

Imperials
Destruction (say Chaos, Crons and Nids)
Xenos (Eldar, Tau, Orks)

... The problem though being, with the preponderance of Marine/Imperial players, having enough wanting to run other armies to have the other two factions balanced numerically against the Imperials. But fluff-wise it was bad enough having the Eldar daemon-summoning prior to the most recent book, but grouping them in the same faction in a campaign really does murder the fluff somewhat.