Hmm, good concept base there. If you had implemented it as it stands i would not have been disatisfied. However i am a bit uncertain abouth the number of psionic vessels, if all their support will be psionic how large percent of their fleet will be psionic in nature then? 2 support cruisers+1 capital ship. I have always been one for quality over quantity for special stuff myself, so im probably predidetermined in this area, so take what i say with a pinch of salt, hehe. I think i would go with a military support vessel based on nanotech myself and give it repair ability as i think that fits perfectly with nano technology and maybe one more non flashy effect. Then i would go with one psionic support cruiser and for that i would use the name shadow as i have i liking to that over say wraith, and i would give that cruiser some fancy stuff like shield target, slow hyperspace etc and then i would have the big ship name spectre is good by the way, have loads of fancy abilities, but little firepower, it should imo be a vessel that is made powerful by the use of its abilities not its firepower. It must be balanced after all, if we want fancy powerful effects as suits the single psionic cap ship of the faction it cant both have that AND powerful cannons. Just my take on things offcource.
By the way i have to ask: you seen the movie PUSH? 
Also noticed that all your ship names are incorporeal beeings somewhat related to death, good stuff there! Ive always been a hound for symbolism.
All in all i very much liked the abilities you set up for your two support ships, they fit well together, i just feel that repair is handmade to suit nanotech even more but offcource thats just a personal oppinion and not at all important.
As for the HQ: 1: i like remote view 2: i like block 3: i dont like extinguish but mostly because i feel its much more suitable for nanotech and because extinguihsing fires is well and good but it its just a tiny part of overall repair. 4: destablice hyperspace is okay 5: teleportation network is okay, i assume it works like the vasari ehr phasegate or whatever its called?
However are you sure you want the building to be a starbase? Would not beeing a starbase require it to be up to speed on all areas to be competive seeing you can only buikd 1 starbase, hmm but maybe its the best idea, altrernatives would be to have it cost tactical slots and so many that you could only build 1 on any planet, like 18, im not sure i really like that however. Or if it was a normal building costing 4 like any other shipyard or whatnot it would need a limit to stop it from beeing more than 1 built at any planet. My biggest issue with it beeing a starbase is probably that it would require a completely new model to really fit well imo, also that i dont really see it as a huge military complex with lots of guns capable of taking on a fleet, sure maybe if it was like THE ONLY HQ for the psicore anywhere it would be fitting, but when every planet can have one orbiting it becomes a little strange to me, but maybe im just a grumpy old man that cant see the sun for the clouds. 
Youll havr to decide, im just beeing quarrelsome here! It could be cool though but the model would need to be awesome! Hehehe.
As for the spectre: incendiary blast is to magic for me i think, would be to much like shooting a fireball and waving a wand and screaming shazam! But it could potentially be done in a nice way if the description said something abouth accelerating the particles to the point where they spontaniously burst into flame and the effect didnt consis of firing out a ball of fire, but rather saw the enemy vessel just ignite with a flame like effect around it or something. Destabilize hyperspace sounds okay, teleport target sounds okay although i dont really see the use for such an ability seeing the game is not really abouth long range vs close range, you get into fire range in 5 sec in any case. in my experience that is. 
Phase manipulation i assume would be the same as armastice? or some ability that just affects enemy targets in a radius with youre own ships beeing able to fire, just not on them? The latest version would be very powerful as you could manipulate so the effect only hit say half the enemy fleet, then you could crush them and take the rest when the effect wore off. An option would be to make the radius cover the entire planet space ofc. That would take care of the problem but it would make the effect do much more than intended.
Watcher: scrying and remote viewing is fine, aura reading i dont like, its is meant to see the auras of beeings, one colour symbolice this or that or simply see their true essence. Well there are several varietys here, but i dont think seeing ships is in direct line with this power. I think here one would rather utilice some form of precognition to sense them drawing near or some form of sensing the ripple in space they make when exiting or entering phase space perhaps. That could fit into several disciplines.
Shadow is fine i guess, i would think shadow would be more closely related to stealth and transportation than actual shield but i guess its a matter of perspective.
Pushers: i dislike the word pushers, because its a oversimplification of telekinesis. Sounds like all you do is push things around when in reality telekinese can do so much more (well in theory lol, i dont personally know anyone who can actually do it) For instance you could reach into someones body and squeese their hearth, or shut off some major artery, pinch shut the windpipe you name it, you could also take part in building projects, lift large objects where it would otherwise require big machinery to do it, hundreds of things, but.. i guess its okay. grumble grumble. not that lifters are any better!
Pyro: i would personally not let the fire discipline do repairs as removing flames is really not the biggest issue when it comes to repair, i would limit it to damaging effects against enemy targets, but not flashy fireballs spewing from ones hands (ships) or some fancy meteor swarm raining down, its all to flashy for me, that i delegate to magic not psionics.
Phase seems okay to me.
That sure was alot of grumbling!
What you have thought out seem so deliberate its more like a finished project than a rudimentary start, i assume you have had this thought out for some time? Or maybe you just have a brain that works really fast hehe. Its hard to make suggestive changes when it all seems so.. done.
On the positive sides i like the setup you have made, the more powers within one line part, some of the stuff i quite enjoy, like watchers. Good stuff there, and i guess one cant get the good stuff without something you dont like. Hehe.
Let me think some on this and see if i can come up with any ideas. But after all my grumbling i must say that it wasnt all that bad, i quite enjoyed it really.
You have to go with what feels right for you offcource, i may like blue while you like red. Make some comments to some of the things ive commented on if you like and maybe a little on how you look at the various things.
