This can be totally misguided, since we don't know if yet again Scott will make Fassbender in total spotlight, but I'm thinking whether there could be more James Franco in flashbacks...I think Daniels dreaming of him could be a good idea, and the dream is becoming very surrealistic and everything is illogically falling apart in the end. Or maybe Franco appearing to be normal and having a normal conversation with her but then says something David would say.
I'd also like the perverted and twisted relationship between Shaw and David to be explored even further so that it'd establish another layer of him being f**ked up to the audience. But it should be not made to make him appear like a clear-cut villain. In the companion book it is said he killed her because he couldn't stand the thought of her leaving him. This should really be explored and not in a 30-second fragment, but I'd love if it lasted like 5 minutes or even more.
However, this all can be rendered meaningless if Scott decides to kill off Daniels or make it again all about David.
I'm also wondering if there will be some kind of a Magneto sub-plot with someone trying to talk sense into David and even making him wonder about all that he had done (like Walter but on a different level)...However, it's very problematic that Daniels didn't have a whole lot of interaction with him to build up on. And Tennessee had none. And thus probably the film will have to be all about David again, right?