Where's Picard's Bald Head...
The mod is great, and I like the fact that you kept the buildlist small and more manageable unlike some overkill mods that just add 50 new buildings to the list and causes players to micro-manage their Cities.... The game play is also pretty great, too, it's unfortunate you dont have a modeler on the team (or do you)
To give a bit of feedback which i hope would help in the development.
production hammer requirements for end-game units is abit low, because if a player had a handful of well developed systems, he can churn out a fleet of Heavy IIs every turn.
In case you're thinking of what to enrich the tech tree with, I suggest checking the old Birth of Federation game, (the official site is already down, but fansites and mod networks are still active) they've got a pretty comprehensive set of future techs.
Furthermore, I was thinking that you can make Unique Wonders for each civ which would skew the civ more to its reality in Star Trek by giving certain empire wide benfits, such as the
Federation: Federation Headquarter that produces
Romulan: Tai Shiar Tribunal that reduces

and gives

bonus
Cardassian: Osidian Order that reduces war wariness
Borg: Central Nexus: no

at the capital and 25% faster military production, -2

but +25%

req for pop growth
Ferengi: The Palace of the Grand Nagus: increased

and war wariness
and so on...
Civ-specific attributes:
Federation: better diplomatic standing with all players, increased growth but higher war wariness
Borg: increased

but doubled

reserve req for pop growth, and other U Bldgs to make Borg Play different
Romulans: increased

but lower

or influence output
Klingons: +1

, but units begin with Attack I upgrade
and so on
World or National Wonders
Transwarp hub (max 3): acts like an airport, but can transwarp 1 ship anywhere
Genesis Project: additional

and creates a Terran large planet in the system built
Camp Kitomer: replacing the Fed HQ world wonder (ST VI: the undiscovered country)
Omega Particle: generates power throughout the empire
Star Fleet Academy: +2 experience points national wide
Section 31: replacing Scotland Yard
Daystrom Institute: replacing Science academy
Particle Fountain Project: x100%

Midas Array: Range of Sight of cities increased by one
Unit Dynamics
Cloaking Device: submarines stealth for Warbirds, bird of prey and available as Attack III level upgrade
Command I: allows 2 fighters squadrons to be assigned (or loaded), a defense 2 upgrade
Command II: a defense 3 upgrade which adds 3 more fighter slots
Construction ship only construct outpost
Consume construction ship with outpost to make space station
Remove the Doomsday missile??
This is starting to get very long, and sorry bout that, most of my ideas and suggestion draws from Birth of Federation, it would be a good reference. If I have repeated anyone's suggestion, i do apologies for the repetition
and I want to see Picard's Bald Head