While its true that the MP/Skirmish factions seem to be untouched no matter whether you play EF or Vanilla, it seems as if none of the savegames are actually copied over from the original to EF.
That means, if I want to play with the Tiger Ace in MP/Skirmish, I'll have to beat that campaign again, first.
Just wondering whether you could fix that? It's obviously not very high priority though.