You asked me a question about the characters, specifically Khan's actions, and I gave you my thoughts on why he did what he did. As for the actors unfortunately there's nothing that can be done about your regret of them not being put in a scene together. As a fan I think I can relate to that sense of regret for many TV shows and movies.
As for TWOK I was fine with the movie we got. Keeping them apart made it unique and I still love the scene where Kirk first gets a visual of Khan while on the Enterprise bridge. His reaction was priceless. There was interaction between them, just not face-to-face or rather them being in the same physical space at the same time. To be fair I can't ever really say if they had gone a different route that I wouldn't have liked it more or better, that's just a hypothetical.