Spoilers for BBS...still reading? ok-
Kingdom Hearts 3 has a shit load of plotlines to wrap up:
*Terra's body (hijacked by Master Xehanort) was erased when Xehanort became a heartless, though what's left of Terra (bound in his armor) doesn't know this and is still waiting for the opportunity to get said body back.
*Ven's body is waiting in Castle Oblivion (in a sealed room only Aqua can open) for Sora to bring his heart back, the problem being, Ven's heart was the same one that Roxas used during the time he was "alive", if the heart were to go to Ventus, Roxas would fade, if it went to reform Roxas, Ven would stay sleeping. Hell of a paradox...
*Aqua's problem seems easiest to solve, she is simply waiting around with Ansem the Wise (who didn't die) in the dark realm for somebody to show her a way out.
*The fact that Sora and Mickey's Keyblades seem to each be halves of Vanitas' X-Blade hasn't been addressed yet.
* Since Vanitas seems to have some sort of leftover power waiting in the keyblade graveyard, it's entirely plausible that the Unversed could reappear in the series, there's also the fact that it would be awesome if he met Sora while unmasked (SHIT WOULD GO DOWN).
Lastly, the english trailer for BBS showed a new secret boss quite identical to Xemnas in KH1 Final Mix (hooded dude with etheral blades), but the symbols on this guys weapons are unknown at this point.