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:
I will have to give the mod a try.
The problem with mods though as you said they are contrained by the orginal programing. Some unquie features of startrek like warp and Cloak just cant be modded in.
That why a Game should be devleoped thats is specificaly for startrek and merges the best features.
Its not hard the tecnology is out there and is being used to create 4X games on a shoe string budget.