I never really thought much about "fixing" Startrek's technology level. I am more thinking about creating a coherent time line (even with time travel in place, it could be better. The 20th and 21st century seem to be a mess), and remove all story elements that were just plan stupid. Transwarp Evolution of Paris and Janeway, Spock's Brain...

Also, fixing and clarifying some elements like "Do they use money? If not, how does it work - accounting for replicators and all that"
They could work to limit some types of technology stronger, more well-defined. As it is, they had to invent restrictions and so on after the fact, if they could go back to the start, the limitations would be easier to build in based on the experience we had - where does Tech X cause a serious story-telling problem?*
*) If someone were to rewrite our universe, he would probably try to limit the capabilities of cell phones. Think back to movies before the widespread use of cell phones and how some of their plots are disrupted if you take the presence of cell phones into account! The writers of reality did probably a much better job with planes and cars - within limits. Hard to tell a 21st century story about a war involving cavalries and trenches... 