Well,where do I need to start?
The Pentastar Alignment is simply too weak.
You should need to give it a few more units, to balance the game. For example makeing the Vengeance-class Star Dreadnought buildabble, and also giving a GC AI to it because it haven't got at the moment...
I'm looking forward to the new features you're creating at the moment...
The PA is no weaker than the other factions; economically they start off worse off, however 2 free SSDs more than makes up for it, and for the same reason them not having buildable SSDs isn't an issue. Having fewer units doesn't make them any weaker either considering they're not actually missing anything, it's just that they have the same units for all 5 eras instead of changing between eras, do at any given time they actually still have the same amount, and keep in mind that the era changes don't necessarily make the other factions stronger. Nothing the NR has in era 1 can even really stand up to a Praetor. And I'd say barring the currently OP Gilzean, the PA also has the best assortment of ground units.
The lack of Galactic AI is not a balance issue, it's a performance issue. In most of the GCs they're in, they do have a galactic AI, however in Art of War for each faction's version one of the other 4 factions has their AI disabled. When you're playing as the IR and NR, that faction is the PA, but again, that's only this one GC. This is explained in several places. This is because EaW is a poorly made, buggy and generally terrible game with one specific bug that causes unit selections and orders to stop working after a certain amount has happened. The more planets and factions fighting for said planets, the sooner it happens. Since AoW has 93 planets, when we had all 4 active, that meant planets changed hands every 2 seconds and it would hit the freeze at week 50. With one faction disabled, it can usually get to at least 200-300, we've gotten as high as 500 without it freezing. It's not ideal but it's a nevessary trade off.