I have not had the time to play the mod yet, but are the goals for each faction?
Well, I can't really translate that into game objectives in the mod, but lore wise.
Empire - Rule all the Galaxy Again
Thrawn - Reunify the Empire under someone
Isard/Zsinj - Replace Darth Vader as ruler of the Empire
Kaine - Undecided, just wants to rule his own Empire for now.
Rebels/New Republic - Defeat the Empire
Triple Alliance - Secure a safe haven for their people to resettle.
Human Trader State - Same as triple Alliance, but allied with Empire and add exterminate all aliens in their territory.
Orthodox Advent - Get the entire galaxy to join the unity.
Vasari Central Command - Unknown, probably either conquer everyone or get enough resources to move to a less crowded galaxy.
So basically in terms of raw firepower, they are the top?
But their challenge is empire management? So late game their faction, if they get themselves together would be the top end faction, assuming empire management.
They are certainly up there, yes.
I don't know if Empire management is there problem. Basically you have this good military force but you can't be super aggressive with it, since if you expand to fast then lose a planet thing can quickly spiral out of control. Basically they take a planet with overwhelming force, secure the area and fortify it to prevent if from being taken back, and repeat by attacking the next planet.
Certain things like Tie Defenders and other cool abilities from the Star Wars lore?
Defenders are one of their unique things yes, but all research is much cheaper and faster for them to get. Basically they're the tech up as fast as you can faction, among other things.
On that note (I haven't uncompressed the game info files), how did the Tie Defender get incorporated? It'd be hard to balance. As a strikecraft, it would be both a fighter and a bomber. It would also have shields. Naturally, that would change balance for the faction.
The base Galactic Empire can only get them from their first hero unit, so they can never have more than a dozen at one time. The Warlords can build them as a regular fighter squadrons but only on specific capitalships, titans and maybe starbase, like TIE Interceptors.
All Advanced Fighters like that will only be able to be built on such unit, and unlike normal fighters they cost antimatter to produce. TIE Defenders will just have the highest antimatter cost, so if you load a Star Destroyer with TIE Defenders and they start getting destroyed, you might find yourself without antimatter to use your special abilities. Hence you probably want to have some regular TIE Fighters and Bombers on each unit even if they can build TIE Defenders.
Strong fighters (save maybe the Tie Defender), and guerilla warfare?
More or less.
Seem like a late game faction, kind of like Vasari Rebel. How would their fleet stand up to top end Vasari or the Galactic Empire once they got themselves together?
Late game yes, but not quite like Vasari Rebels. I can't say much more than I already have since they're the last faction to be completed and thus not quite as planned out as the rest.