The entire EU will be neatly sorted out in Dark Horse Comics forthcoming mini-series:
Crisis On Infinite Nerfs.
Oh well played Sir. Well played indeed !
And for what it's worth, I can't see the new continuity taking in another civil war, the Vong or much of anything except maybe a few characters and very general ideas such as Mara Jade and her being 'The Emperors Hand'.
A pro screenwriter just wouldn't bother reading the EU, wouldn't want to be constrained by it and would have some pretty specific story instructions from Disney to boot.
I'd expect some carry through from Clone Wars though - maybe Ashoka and Ventress, plus a return of most of Mace Windu.