Minas Morgul is horribly boring, and there's no real action happening there (Witch-King's major moment is on Pelennor), so it would be a waste. For the same reason I don't see Barad Dur, there's no scenes in it.
I still think we'll get the balrog, the Witch-King, probably a stand-alone Treebeard (as they specifically didn't name the Orthanc ent). Meduseld would be completely awesome (and include tons of characters), but I'm thinking it's too "boring" for a Lego set. There's not many action features you can include (except flick missiles in the throne), although Hama and Gamling would be cool. Something from Minas Tirith also seems a given - especially now that they have two sets to bookend the Pelennor battle.
For The Hobbit or both movies, Rivendell is still possible. We have two Mirkwood sets already, but Thranduil needs a reason to show up. Then it's quite likely that we get Laketown and/or Dale, something Dol Guldur, something nazgul tombs (with catapult to throw Radagast down a chasm), and one or two Smaug/Erebor related sets. Oh, and Beorn, most likely. And a Five Armies battle with like two soldiers on each side.