Considering this is an early-stage release of this mod, it's outstanding!
I'm one of the folks who don't mind some of the liberties taken with traditional star trek lore (and it's ok if you're not! There's fantastic mods to accommodate both camps between this and SoA2). I love that this has Titans. 
I'm pretty excited to see future releases of this mod.
I really like how you guys handled hero units. Having only one ship with the iconic captains' voices is a nice touch.
Janeway's ablative armor ability. Holy SHIT. Impressive. I looks just like it did from the show. Very well done!
Some feedback after spending several hours yesterday in a long game as federation with a Klingon AI ally vs. the Borg (I understand that some of this might simply be unfinished at this point and known):
I notice that while very much like E4X's hero system, the hero-summoning structure in this mod is not invulnerable. Is this intentional? I could see it going both ways. It's kind of annoying to lose an irreplaceable structure, though.
Some of the pacts between faction share the same name but do different things. That's not *bad* (more bonuses than if they WERE the same) but having unique names would be nicer.
Regarding ship balance:
Some of the caps seem WAY more useful than others. I am admittedly biased in favor of the Sovereign (probably my favorite star trek ship) but it seems especially useless in this mod.
Especially when facing the Borg, it's all about armor/damage reduction/hull repair (or, of course, massive debuffs). Shields are almost useless. Most of my caps died with 80-90% shields.
By the last third of the game when i finally went on the offensive, i managed to liberate a dozen Borg worlds without a single loss (while killing a bunch of unicomplexes and countless cubes/diamonds/random borg ships, eventually getting my all-cap fleet to levels 8-9) using a max-cap fleet of: Titan, even mix of nebulas/phoenixes (the bulk of my fleet), 2 galaxies (just for the AE debuff) and one Ambassador (to colonize the worlds as i go). The Ambassador is obviously the weak link and is just there to colonize, it's shield-heal (while probably very useful against non-borg) is useless in an anti-Borg fleet.
The phoenix's (or was it nebula? i get them confused) high damage reduction for itself combined with its high hull repair for the fleet makes it critical against the Borg. The nebula's shield-disable ability is right up there, too. In one ability it reduces the duration of the fight by more than half.
The Galaxy's good damage and AE debuff are nice, but not really essential. Once you're rocking the 'holy trinity' of Titan/Phoenix/Nebula anything else is just extra. Which really seems to be the problem. The Galaxy at least has reasons to use it, but the Sovereign is pretty weak in comparison. Every one i built died, so i just... stopped building them.
On that note the TL titan abilities from the base game on the Fed titan are PERFECT for an anti-borg Titan in this mod, heh. Get rid of the red bars from the FD visual effect and that ship is done. 
Regarding ship flight:
This is probably a polarizing issue, and i know SoA2 does it as well, and i get why. It looks really good pre-rebellion, at least. I am of course talking about the 'always fly around like a fighter' aspect. It really does make the game look more like the shows/movies, i'll give you that.
But it's got some glaring drawbacks (most of which apply even pre-Rebellion).
1) The Rebllion issue where a ship will fly out in a straight line seemingly forever. Saw this countless times, yesterday.
2) Once i got a large fleet going, they looked like they all had the worst navigations officers in the universe. They were playing bumper-cars in space.
2a) Not sure if it's related to 2 or it's own issue, but i often saw ships flying REALLY close to the borg ships and parking there. My fleet would be shooting a cube and they'd all be bumping up against it. I dunno if it's related to the flight issue, or a range issue, or something else.
3) Probably the worst offense after 1): Ships that DON'T have banks of weapons in every direction take a significant hit to their damage output and gain nothing. In the shows/movies the REASON ships fly like that is for evasion. In the game, they gain no defensive bonuses for doing it. They just lose out on damage. Take the Defiant. It's crippled by this. Even ships that can fire in all direction still take hits, since their forward-facing banks are usually the strongest.
This isn't easy to fix, either. You can't just double the DPS of the Defiant, for exmaple, because then if it's got targets in multiple directions it's suddenly doing way more total damage than it should.
Same for other ships. You can't make all their bank identical, it'd a) look bad and
make them all massively overpowered in large engagements.
Has NOT using the fighter-flight characteristics been considered/weighed, at least?
ANYway, wouldn't have typed so much if i didn't love the mod. Keep up the great work, guys! 
EDIT: Spelling and typing, how do they work?!