About HLAs: I personally think that every specialization should have at least 1 special HLA for them. Ideally T3-T4 ability to get. If you kept basic HLAs that you've already made but gave special for each discipline it would make them even more distinct and add a lot of replayability for this mod. You may also decide to upgrade just one ability through T3-T4 that would make it nicer as psion progresses through the game and would save you a lot of work from making new ones that could prove obsolate.
Here are the suggestions as follows:
Seer: Each power may focus on different immunity (elemental, saving throws, AC, physical damage) or rather make it more offensive with bonuses to tHAC0, damage, maximum rolls for dice and work either for entire party or a single character (depending on decided approach and balance).
Shaper: This is easy and it may focus on creating better and better construct.
Kineticist: If you don't want to make Dragon Breath-like power then I have no idea Maybe Elemental Ball like 3.0 epic spell dealing 10d of each type of energy? Still, it's weaker because in 2.0 there is no sound damage. I think it wouldn't be op for T4 as most enemies in ToB are immune to certain elements. Progression through this HLA could focus on improving dice (d4, d6, d8) for this spell and saving throws to half the damage.
Egoist - Bhaal's avatar ability somehow solves the problem of non-able to fight casters but maybe addressing it in HLA would be a good idea (I'm not sure if you made one already, I didn't play as Egoist yet). Psion morphing into ultimate killing machine for a while and for big pp cost and probably with extra post hoc power cooldown may be a nice posibility as Tenser's Transformation (as far as I remember) never was that strong, which makes Psion even more unique compared to mages.
Nomad - Boy, I have no idea
Telepath - Something like Mass Charm with upgradeable ST through progression. Or maybe the way to charm ANYONE (if engine permits) for 1-2 rounds.
About items: I imagine Psions as beings with extremelly strong minds, I think items could focus on improving that aspect of psions to fit that description. Bonus to saving throws is one option. Another option is a (maybe upgradeable via Cespenar) robe for each specialization as follows:
Seer - Aid-like party power 1/day for a couple of rounds. Upgrade makes power stronger.
Shaper - Better AC (3?). Even better AC (1?).
Kineticist - Percental immunity to elemental damage (20%?). Higher immunity (30%?).
Egoist - Tenser's Transformation-like power or percental physical immunity for damage.
Nomad - Ability to avoid death when in trouble (20%- hp). Sequencer-like power that moves Nomad to random safe place nearby protected by Invisibility. Improved invisiblity + heal 20 hp.
Telepath - 1 point higher ST for certain Telepathy powers. 2 point? Or maybe short-lasting domination-like power.
Basic bonuses would be: AC 5, bonus to saving throws: 1. And for improved version AC 3 and bonus +2 to saving throws.
Extra question: Do you plan to add Psychic warrior class to the game?