These may already be fixed, but please check:
1) Yor did not have access to the telepathy center / insta-flip building. Is this supposed to be this way? I really like having that.
It is supposed to be like that. Yor have access to No Mercy Invasion Center, Drengin to Mind Control, Korath and Drengin to Artificial Slave Center. Overall Evil is not as strong as it was. Maybe even is weak
Generic Good civs have more extra techs if they stay Good after picking Xeno Ethics. Maybe generic Neutral and Evil could use an extra tech or two if they stay in their Alignment, just as Good races do.
As far as I know, Evil civs pick Ethics late, and usually have superior weapons anyway, so any advantage they can get from this tech is lost. Sadly, this makes weapons from Evil alignment to be only utilized by the player. Good races at least can get +25 Creativity and +10% Planet Quality, even if they already have better defenses (but usually they don't). Not to mention Starbase modules are cheaper, making Evil even less attractive.
Altarian: Shrine of Mithrilar - it is quite weak for a Super Project, and AI tends to build it on bonus tiles. Both Manufacturing and Research could be increased to 12 from 6.
Torian: Aquatic Transport Station - it can be safely changed to SP instead of GA. By the time you can invade Torian HW, range should not be an issue anyway. Changing it will let multiple civs using Torian tech tree to get this improvement.
All most powerful Invasion Tactics have drawbacks - Tidal Disruption will most likely destroy everything on the planet, including those yummy improvements on Iconian worlds. So you need to invest in the planet first and start building your own improvements.
Core Detonation and Mass Drivers can both lower the planet quality, and also destroy improvements.
In vanilla, the only clean invasions were Traditional, with no bonuses, and Mini-Soldiers with a bonus 40-70 for 500 cost.
Both Yor and Thalan had no other invasion tactics, except Gas, Insurrection and in case of Yor, Mass Drivers. Two newly introduced invasions are just too strong for their clean factor. Thalan were supposed to have harder time with taking over enemy planets by force, as they had lowest Soldiering just before Iconian, and Yor already have +30 racial ability, so they do not need to be too OP. Space Marines unlocks another strong invasion tactic, Marines, which also is very clean.
Marines should be an improvement over Shock Troops, so 70-100 should stay. Cost of 500 is also appropriate. No changes.
Mechanized Warriors: Producing Mechs should be more expensive then training marines. Also, this tactic is too strong as it has no negative effect on the world. Suggested changes: 700 cost from 500, attack 60-100 down from 120-150.
Terror Drones should also cost more, as these are high tech machines. Cost 700 from 500, attack 40-120 down from 90-120. AI is not perfect, so they should be unpredictable. Improvement Penalty 5-30 from 5-10.
I ran 6 games with Iconian, Thalan, Altarian and Drengin. Medium, Normal tech, Abundant habitable, Common planets, Scattered. Occasional Extreme.
1st game, Iconian dominated, Thalan second.
2nd game, Iconian and Thalan. Drengin had best starting position but were barely keeping up with Altarian.
3rd game, Iconian, Thalan and Altarians second.
4th game, Iconian, with Thalan and Altarians both second again, Thalan starting in bad spot.
5th game, Thalan, with Iconian second.
6th game, Thalan and Iconian.
Altarian still don't build enough labs on their planet. Every second planet is filled with Industrial Sectors, which they almost always get, but except for 1 or 2 pure research worlds (and HW), they hardly have any labs. So even with 60% research spending, it is only half of what Iconians and Thalans have. Also, their economy almost always crashes for first 50-60 turns, after it stabilizes, they are so far behind there is no chance of them keeping up with Iconian or Thalan.
Iconian performance can be attributed to good combination of their 1pp improvements - they always have 16mp Refinery, so they can build/upgrade their improvements quite fast, and Precursor Archive on every planet helps with their research a lot. They never had a bad starting position, and are able to get more planets then others, thanks to moving x-col past Terraforming. Their research/manufacturing goes up and down just like Altarians, but once they get their 1pp economy improvement, it sky rockets.
Thalan twice had bad starting positions, but were still doing very good. They don't have the best economy at the start, but it's best to leave it like that as I fear any improvements in that area will result in godly civ. It's good they are tamed a little bit. They almost always get Gravity Accelerators and Hyper Computers first.
Drengin are doing badly. Even as they had best starting position of all in one game, they were just "meh". Maybe cost for their research labs should be lowered down to vanilla - 100 for Diabolical, 400 for Imaginative and 1200 for Ultimate. Their labs are in line with vanilla progression, so it's cost maybe should be lowered to be more like in vanilla as well. Another thing is, they don't build enough manufacturing and lab improvements, sometimes leaving bonus tiles empty and building Arenas instead. Worlds like this happen too often: