I feel this fugitive Banner thing where he's always on the run from the military and secret organisations has been done enough. (My suggestion was about Banners protection, so as not to confuse this as contradiction)
My feeling is that Banner will spend half of his time crying, and the other half of the time trying to resolve his problem. But how will he go about this?
We'll need to look at the personality of Banner a little. Coz I don't think he's as simple as we immediately presume. We have to do this to really understand what he will do next.
Banner states, supposedly posthumously, that the Ultimates were the best friends that he's ever had. So we can gather from that that he's low on the social skills area. But wait-a-minute, Betty Ross is a fine looking woman. And really, because we care so much about the Banner character, is this because he's a loser, or is it because he's actually quite charming? I think it's the latter, he has the charm or a spoilt child, and the tantrums to prove it. We feel pity on him, yet I feel he's perhaps a little more controlling (in that childlike way) than we have actually given him credit for.
So what will he do next? I feel that Banner has a jeffrey dahmer*type personality here. He's introspective and quiet when he's alone, but when he is on a mission, then he can be as charming as anyone. You think he got to be head of the SHIELD supersoldier program simply because he was bright? He would have maneuver himself into that position, because it was his dream. The polarity of the Banner character in himself, if far more interesting that the Banner/Hulk dynamic.
In the 616 universe, Banner cannot control the Hulk, it's his curse. I feel that in this universe, the Hulk is his way of absolving himself from responsibility of his actions, his tantrums. And through this, I feel that he will be able to control the Hulk a lot better, and induce the Hulk when needed. We know that Banner has turned into the Hulk a few times while in confinement, who are we to say that it was not just some way of seeking attention?
Frankly, Banner is a charming weasel.
So, if this is true, what does banner want to do next?