First of all, I really like the amount of diverse skills and their reworking, but I do have some points I would like to note:

1) Vitality. I often skill the first level of the off-skill mastery in order to gain more vitality (so, melee for a sniper for example) if I have enough points over (basically no other skills I really want).
I would rather see Improved Vitality be a sub-skill of the default vitality, instead of forcing you to choose (I generally regard First Strike as very important when skilling melee, for example, that I choose Improved Vitality near to never). It does mean that there is a need for two new skills for Melee/Ranged Specialist, though...

2) 'Heroes are not affected' skills. I kinda agree with the thought behind it, but I really, really hate that it does not affect the leader either. Skilling Offense, I often keep at level 1 to get Infantry commander when having too many heroes in the army. Or when my units are not the damage dealers, etc.

3) The replacement skills for Offense/Defense I quite like, but it feels like 'Voidtech' option (Robot Commander) is out of place (also applies to Promethean, but heavy units tend to be more often mechanical, too). First of all, it replaces infantry Shields, and Voidtech actually does have one Infantry unit (albeit the first one only). It is especially jarring, when you don't have the VoidTech secret tech. Mechanical units are already few, and non-mindless even more so.
Well, its not a big thing, its just something I found few applications for so far (especially because I tend to stay low tech).

4) I dislike having two 'army leader' type of skills in the same tier. An example is Xenoplague T2. If your hero is no army leader, both skills are useless. Ideally, each tier would have at least one ability that does require the hero to be leader.
The same is applicable to the tier skills. A celestian or psynumbra are only really useful if your hero is actually an army leader as well. It reduces the modality of your army compositions. The biggest offender is IMO the Heritor skill, because not only does it need to be an army leader, it is nigh useless outside of Heritor Secret Tech, too

and finally 5), skill balance.
So, lets first talk about Secret Tech ultis.
- VoidTech is a very very strong ulti if you are not melee. Extremly powerful IMO.
- Xenoplagues regeneration ability is also very nice and useful.
- Synthesis is also very strong, but needs to be army leader. Since the effect is quite powerful, though, I do think thats all right.
- Promethean I haven't played with it, and while 3 APs seems like too high, I don't know how it plays, so I will not comment on it.
- Heritor is based on a skill that wants you to have the Heritor Secret Tech anyway (because the Essence Charges are not as useful otherwise), so I guess it is more specialized. Again, I haven't really played with it, so I don't know how powerful having more essence charges truly is.
- Psynumbra is quite interesting, but also wants you to be Psynumbra secret tech (osynumbra units and the doctrine that leaves behind an echo when a psynumbra unit dies). It also doesn't help that you are forced to not only pick, but also use Devour Hope to attain your first Echo, which then needs to use it as well, etc. Its not a high pick for me in general, and I don't feel like I really want it even when I am Psynumbra either.
- Celestian feels terrible. Mainly because the Soul Shield it is based on feels terrible. First of, if you are not celestian, your units tend to not be Enlightened. Secondly, the Resurgance is time limited. You kinda need to somehow sacrifice it while also being useful in some way, and finally, there are a lot of ways to grant resurgance, including attaining prime rank. It feels like the worst Ulti, because even 'improved', the skill will eventually loose its relevance, is very restricted and does not enough to be worth it.

5.1)
So, having talked about the Ultis, I want to t alk about specific skills. I already mentioned one that feels extremly underwhelming:

CELESTIAN
- Soul Shield: IMO it should be redesigned, to first of all grant Resurgance until end of battle, regardless if the friendly unit is Enlightened or not. Additional, if the Unit is Enlightened, it would gain Last Stand for 1 (2 with ulti) rounds.
- Revealing Soul: It is the only way to apply Soulburn outside of the Secret Tech, and it feels ... not good enough at all. Especially, when your hero is in the back (I play a celestian sniper). It makes it far harder to actually apply Soulburn to anything. I realize that it was a vanilla skill, but I think it needs to be better. At the very least, let it also apply to the hero's attacks. Especially since Cleansing Light is a very useful skill.
- Deny the Wicked is fine except that, as I already mentioned, there are far too few ways to actually inflict soulburn outside of the Secret Tech.

PROMETHEAN
- Purging Field, if I understand it correctly, should be a 1AP ability, and not a 3AP ability
- Extermination Squad / Fallout Protocol are both army leader abilities. I would like to see Purging Field and Extermination Squad's position to be switched
- Chemical Additives: Mechanical units are few, most are either biological or cyborgs. It feels too narrow, and it can also damage your own troops.

PSNUMBRA
- Inescapable Echoes: It is too narrow IMO. If you don't have a lot of ways to Fill the enemies with Despair, it is barely useful. I would like to see it also change the Devour Hope ability if you have taken it (which seems like something that you will if you want this skill anyway) so that the Devour Hope leaves you one point instead of ending your turn.

SYNTHESIS
- Electrifying Subroutine and Assisted Breach are again two Army Leader abilities in the same tier. Both are very strong, though, and hard to redesign. Maybe allow Assisted Breach to also effect when not Army leader?

VOIDTECH
- Instability Generator is a very narrow ability, although probably quite powerful in the right build. I get that it is mainly to help to apply dimensional instability.
- Stasis Field looks quite weak to be honest. It has a decentish range, but it consuming your turn is rarely worth it. It does also only immobilize, making it a weak choice against most ranged units. I think giving the ability something similar to Dimensional Desync would be more interesting.

XENOPLAGUE
- Spore Feeding and Intuitive Evasion are, again, two Army leader abilities on the same tier.
- Caustic Smoke feels a bit weak as a T3 skill. Low range, low damage, and basically the ability of an Engulfer, which is an early T2 unit.

HERITOR
since I have not yet played with an Heritor, I won't be able to comment on the skills, but I do think that the Essence Protection skills are only ever useful when playing as Heritor, which is a bad sign.

GENERAL SKILLS
Piloting, and especially Advanced Piloting, have always felt ... overpriced. I rarely go for Advanced Piloting (it costs 8 points! The highest c ost of all skills!) if I don't find a good T4 vehicle. I personally would suggest:
- Tier 1 Vehicles can be used by anyone without Piloting skill (are there even any?)
- Piloting costs 5 points (still) and allows piloting T2 and T3 vehicles
- Avanced Piloting costs 3 points, allows piloting T4 vehicles and grants regeneration (?) [in that case, Field Repair Droid would grant not regeneration, but heal for a flat amount, similar to Self-Repair Systems mod] or something else.


I haven't yet mentioned the Race skills and such, and may do so later. I would like to discuss these skills first, because I may overlook applications for it that make them better than I thought.