I would suggest making all such event designs somewhat fluid rather then rigid .... requiring less rigid thought process in certain aspects of design, anyhow (for practical reasons). The war can still be won or lost by one side or the other but the players can still move about and the medals can be awarded for specific achievements on either side. This leaves room for both the conventional wargamer, who could pick a side, even a unit (for a time) and stay statically immersed to try to enjoy a specific "character career" (if you will) ...
and ... the player who wants to experience some diversity throughout the campaigns as they unfold (perhaps even being the sort who volunteers to switch sides, for balance sake, on a regular basis anyhow and merely enjoys the game for it's mere dogfighting qualities).
I don't really see pre-registration for the entire event as critical as, say, a good design involving an evolving war. Have what the players do in game affect the industrial and development aspects of their opponent's side as each month (or season or year) of the war unfolds (in each theater). Bombing certain factories could slow production .... or create a setback in developing the next fighter or bomber or tank to be released. The factories can be delegated for specific duties by the command groups (of course, in secrecy and, most probably, selected due to their difficulty in attacking). Command groups could also dedicate limited information gathering resources to determine the best strategic targets to attack (this could be simulated between groups utilizing online random number "dice" generators for success in determining precidely what factory is working on what).
Personal glory can be custom designed to the player's desire. If they are dedicated to making it a win for the Allies or the Axis, their uniform reflects ... well ... uniformity in it's salad. If they are more dedicated to being the ones who fill in (granted, having pretty much no access to the upper level of strategy for one side or the other) then their salad is mixed (tossed, if you will).
Sure, as illustrated, any player that plays "balancer" or prefers such diversity should say so from the beginning and not be part of the command structure or planning group of either side .... and .... conversely .... all players who want to have a role in developing the tactics and strategy of either side should remain loyal to it (unless a "turncoat and traitor" aspect is to actually be incorporated into play).
Argh. So much for kibitzing from the sidelines. Go Navy!