I agree that the later ExU sucks big hairy donkey... you know. However, most of the Expanded Universe fans love the early post-RotJ series of novels and comics... The later stuff is what most people dislike, and the whole "Starwars Ball Z" feel of the "Ultimate Power Luke", etc. can get blasted for all I care.... along with all of the crap from Karen Traviss. She's a good military fiction author, but she sucks horribly at Star Wars.
Seems you verified what I suspected NJO sucks
So i think the solution is clear - say the NJO era didn't exist, that would give Disney and Lucasfilm the perfect playground to work with. And their actions would not affect the previous good stuff that you mentioned alone. And seeing as support for the NJO era is minimal, they can get away with pretending it doesn't exist and carving out their own chunk of space to work in. Not sure about the whole timeline thing, but this may lead to the death of the whole Darth Caedus/Lumiya arc - I don't know.
No matter what happens, look on the bright side. IF they go with the three universes, at least it's not as bad as in comic books. 52 universes in DC. Hundreds of universes in Marvel now, since they adopted DC's "multiverse" idea.
Slippery slope, 3 will become 52+ before you can say Yuuzhan Vong...
At a push i could except an alternate NJO era - but labeled as non-canon (like starwars infinities) Thus in a canon-sense that era could be erased and the films accompanied by fresh EU can take its place.