Well, that's pretty much what people making mods did. Plenty of mods for BotF, even though that game suffers from bad design.
Space Empires 4 has a mod which is very close to true trek experience. I personally made modifications to it, including a more accurate galaxy map, more trek races (like Xindi or Terran Empire), but that game too has problems, especially because there's no true warp travel, moving is done by going through wormholes from one system to another and development is very, very slow. Otoh, one could design ships from scrap and equip them with any equipments he/she wants and name it too.
If only there was a way to merge the 2 games, the result would spectacular.
I still have some old screenshots of that game: