The current brand of Batman is far better done and put together than any Star Trek movie out there.
That's also true of his movies compared to most of the previous "brands of Batman," though.
Unless Nolan can move now to directing only original material while maintaining his career at these heights - possible, but far from certain - he's going to be "slumming" again in one studio franchise or another, sooner or later. Very, very few directors of this generation avoid it.
And as I noted, he also produces
films like Superman. He could easily wind up producing Star Trek.