If I understood my "gamelore" correctly then Bhaal is trying to pull a "Mystra" on the realms. Hence he has instilled portions of himself into mortals, his many children to be precise. With each death of those children a small portion of the "fallen" god is added to a whole that presumably is the old god himself.
I would assume that the most evil and destructive of his children will be the vessel for his return. An evil god would like to inhabit the strongest and most potent body around. In the dream sequences in BG2 we learned that the protagonist is "strange amoung his kin", being able to remain free of will and succesfully resisting the possession of Bhaal. Heck! Even without a soul the protagonist manages to keep the "instinct", aka The Slayer, under check.
I thus make the prediction that in BG3 the protagonist will be the among the very last surviving children of Bhaal, with Imoen still being the trusty sidekick of course. Bhaal will return to the realms wich will lead to a disaster of cataclysmic proportions when the old god heads straight into battle against the younger and more powerful god Cyric who was the one who killed Bhaal the last time around.
This causes the protagonist to be faced with a certain dilemma. Bhaal is not whole, lacking the essence of the VERY powerful protagonist and Imoen (The levels reached in BG2 and the possible expansion makes these two the stuff of legend in AD&D) wich leads to an almost desperate hunt for these two (since he needs all the power he can get in order to face Cyric). Imoen will most propably die, I would guess that she sacrifices her own life to save the protagonists, and thus revenge is added to "motivation stew".
I strongly doubt that the protagonist will rise to godhood but will instead destroy the immortal portion of his or hers soul that carries the essence of Bhaal. Bhaal gets his butt kicked for the second time by Cyric and the protagonist is able to live out the rest of his or hers life in relative peace.
- So it is written and so it might just be.