Likely one of the first things I's be inclined to do is update the ship schematics. The current drawings are simplistic representation of the various ship class, and while a lack of detail could be excused for the sake of reprinting such small drawings the shapes and proportions could definitely be improved.
I'd also toss out the Microgamma font for ships' registries since that's definitely not what we saw onscreen. All the existing drawings of interior facilities and equipment would also have to be revised. For the hangar area has anyone seen MGagen's
3D work on Hobbytalk? I highly recommend checking it out. He takes the pylon support structure into account and yet still renders a flight deck that looks very much like what we saw onscreen---really nice work.
There are a number of really good efforts at fleshing out the deck plans of the Enterprise
around the web over the years. For myself I'd be inclined to ask permission to mine the best of each. I've also seen some fabulous croos-sections including aridas'
The uniforms section would have to be expanded to include Cage era uniforms. And then we get into an area left blank by FJ, alien ships and equipment and uniforms.