Well, Obvious "unfinished things" would be:
3) Where goes the rest of your crew, like T3M4, though we know about Remote/HK/G0T0. The whereabouts of Visas and the rest during the M-V incident would need some explanation.
2) Bao-Dur, and his Importance (though we could have guessed it with remote, but what of Bao-Dur?) Though maybe they want to make Bao-Dur reappear in the third game.
1) HK and him mentioning of the factory, definitely unfinished part DESIGNED to be in the game.