My personal theory is that very soon Hancock will be found as a traitor (or useless to the Shichibukai) and will be hunted. As Luffy's still recuperating, but awake, Pacifistas and maybe one big boss (DoFlamingo's my bet) will come to kill Hancock. The Kuja's will fight bravely, but be overpowered, when the Strawhats appear (how? See link in my sig).
The Strawhats will kick pacifista ass, showing their growth.
Hancock will fight the big boss, her secret will be revealed to the kuja and, while she's mind-raped by DoFlamingo or whatever big bad is there, that will make Luffy angry and take him out of his apathy. Luffy attack the big bad, but due to wounds Hancock will rejoin the fight and together they beat him.
The kujas won't care about the slave mark and will still want Hancock as empress. She will be thorn between duty and love. Seeing this, Nyon, her sisters and the kujas will encourage her to be happy and go with Luffy. Cue Hancock's real original dream and she going with the Strawhats. Awwwww :wub:
Or something like that.
Usual disclaimer: just a personal theory, and a little more probable now that we're heading to AL and Ivankov's going to Kamabakka, where he may find Sanji and tell Luffy's whereabouts.