Ok, now I finally have time for an in depth response to the OP.
The purpose of this thread is record all balance issues in one place for easy reference and then to suggest changes. Here I'll list some examples of possible solutions from my own ideas and also ideas that have been floating around on the forums. Ideas that are not my own (which is most of them) are marked with an asterisk.
Any input would be greatly appreciated.
TEC
Kol Battleship:
Gauss Rail gun ability could benefit from a better secondary effect. For example, a nice buff could give this ability the effect of temporarily stopping passive regen on the target.
A secondary effec would be nice, but it would also go a long way to simply reduce the antimatter cost GRG and make it's cost not scale up with level. GRG adds very substantial DPS if it can actually be spammed, but at present it runs the Kol out of AM fast.
Adaptive force field should be rebalanced as a passive ability*.
This is a great idea that's been floating around the forums for years and would be easy for the devs to do. I'm in full support.
Honestly the other change to the Kol I'd like to see is a buff to give Flak burst some early game usefulness. The idea I've had for some time was to have flak burst flat out destroy maybe 2/3/4/5 nearby enemy sqaudrons, then deal it's damage to any remaining enemies squadrons in the area. That would give it a major impact early game, and at all stages of the game guarantee that each flak burst immediately reduces the brunt of the incoming bomber swarm at least a little.
TEC Loyalists
Hardened Defenses should be moved down to tier 2.
Honestly I think there are better techs to improve for the TEC loyals. Hardened defenses isn't worth it's current tier, but even if it were improved it's not ever really going to be a very high impact tech(being that early game tactical structures are already pretty beefy and built in small quantities).
Improving War Measures Act or Battlefield promotion be be a large enough bonus to actually create a noticable defensive advantage could have a much greater impact of the game(think of what it would mean if long drawn out unsuccessful sieges meant giving the TEC loyal player a decisive economic or capitalship level advantage over the attacker).
Heck I'd also love to see militia weapons/armor get a base rank 0 value(like the advent frigate respawning techs). this would mean TEC loyals would be stronger at defending right from the start of the game with 0 techs researched. Perhaps something like 10% of militia weapon's damage and 1 armor from militia armor as a base value(with the per rank bonuses reduced 15%->10% & 2 armor->1.5 armor resulting in the same total bonus at rank 2 of each tech).
Ankylon Titan:
Group Shield should have its cool down time greatly reduced, possibly by as much as half*.
Reducing the cooldown would certainly help. That said I'd like even moreto see Group Area shield also restore maybe 10 shields/sec to affected frigates. Part of the reason the Ankylon's fleets can't survive late game fleet battles is because even with 85% damage reduction they need both full hull and some shield points to survive late game enemy titan AoEs. In the 30-40 seconds between titan AoEs hoshikos replenish the needed hull points, but at present the TEC loyals have no reliable way to recover the needed shield points after the first titan AoE drops their entire fleet of frigates to 0 shields.
Furious Defense could inflict 20/40/60/80 splash damage with 1500 range when active.*
This would certainly be a fast way to make the Ankylon strong. personally I'd prefer to shoose a method that keep's it's uniqueness as a fleet support titan, rather then make it viable by scrapping it's identity and just turning it into another AoE monster.
Honestly I'd rather see something done with Furious Defense to address how vulnerable the Ankylon is to being AM-drained then ignored(do to it's Low DPS and lack of passives and inability to frontload enemy casualties before it runs out of AM via strong AoE).
The idea I've been thinking about was something along the lines of:
Furious Defense(Change to a passive ability): While the Ankylon has at least 95% of it's hull points it regains 1.5/3/4.5/6 antimatter per second. When it drops below 95% hull this antimatter regen stops and is replaced with 15/20/25/30 hull regen/sec or 30/40/50/60 hull/sec in a friendly gravity well.
This would essentially mean the only way to keep the ankylon AM-drained would be to focusfire it. if you ignore it, it will keep supporting it's fleet all day.
Inspire and Impair should effect SC.*
I'm in full agreement here. It's a titan level 6 ability, something that will never be present before the late game. it really should affect the quintessential late game unit, the bomber.
Advent
Mass Disorientation could effect SC.* I quite liked this idea when I first saw it although I am skeptical as to its necessity. EDIT: Instead, this should simply be non-interrupt able; suggestion by Seleucia.
Honestly as much as my inner advent-lover would adore this change, I suspect it would be too strong. The Transcendia is already the strongest defensive starbase(and for that matter between extra strikecraft squadrons & meteor swarm already the best at dealing with starbase counters such as anti-module frigates and bombers). If Mass disorientation affected vbombers it wouldn't really have any counters as it would lock down entire swarms of bombers outside their weapons range for a minute at a time.
I like the idea of preventing it from being interruptable though.
Allure of the Unity should be tier 2.* It gives only a 5%/10% allegiance boost to planets and yet is tier 8. Currently not worth it. Should also be just 1 level; suggestion by Seleucia.
I think it would be a better idea to make it T5 or T6, but only 1 rank. AT present there is very little reason to actually go past 3 harmony labs. 1200 credits for +10% allegiance at all worlds would be a pretty compelling reason, and would still be a pretty nice boost to the advent economy.
Maybe reduce the tier on the advent Loyal's Global unity though so they get extra allegiance a bit earlier.
EDIT: Final Judgement should target enemy cap ships and Titans; suggestion by Seleucia.
This would be a really cool adition and allow a neat, but underutilized ability to take the spotlight.
Revelation Battlecruiser:
Guidance should grant a 20% range buff to all allied units.
And interesting idea, but I doubt it would make the revelations worth using. The main threat to Advent starbases are bombers and +20% range isn't going to let the starbase hit carriers on the other side of the gravity wells.
I've always liked the idea of turning Guidance into a focusfire ability, similar to the Cielo's Designate Target or the Subverter's Shield disruption. This would be a natural combo with Reverie(Put one capitalship to sleep and focusfire another capitalship or titan or starbase with Guidance). Not to mention it would make the Advent heavy Assault ship actually good at attacking starbases, something the advent has always have trouble with. Would synergize well with the Coronata as well giving Advent Loyals a boost.
Perhaps something like:
Guidance: The revelation coordinates the assault on target enemy The revelation grants all nearby allies +5/10/15/20% accuracy and the targeted enemy takes 8/12/16/20% extra damage for for 25 seconds.
Cooldown: 30 seconds
Am cost: 60
The accuracy bonus is merely to keep the abiltiy somewhat multifaceted rather then just a boring "20% damage". it would also help Advent Flak shoot down fighters, which most notably would help in assaulting enemy planets who's hanger bays field fighters that threaten the Advent's only effective heavy assault strategy: bombers. So both parts would contribute to the Revelation's primary role as a heavy assault ship.
Advent Loyalists
Global Unity should be moved down to tier 3. Deemed unnecessary by GoaFan.
This would be nice, but I'd much rather see Assimilated populace dropped from T4 to T2 or T3
[EDIT: but I see you've already noted this opinion in your OP]
Assimilated Populace should grant its effect upon use of Repossession*. It is ridiculous that a faction whose theme is synergy has upgrades that are designed to not synergise.
I agree fervently
It would be as if the Eradica's Purification ability didn't activate the buff granted by Strength of the Fallen. Drop this tech down two tiers; suggestion by Bilun.
Upon initially writing this post I had entirely forgotten I had already given that bit of feedback in my minimal post; I feel a bit silly for repeating myself above 
Coronata:
Subjugating Assault: This should grant the same amount of exp as when a target is destroyed*.
Agreed again
Suppression Aura should effect SC or possibly corvettes instead but this would probably require a stat nerf so that the debuff that it grants isn't so large*. A passive 40% damage nerf and ~60% speed nerf to enemy bombers might be excessive.
My thoughts exactly
Repossession should reduce the price of planetary upgrades by 33%/66% instead of 0%/33% as it is now.
I'd be satisfied with just assim populace affecting repo- but this would be great as well. Anything to make Repo less circumstantial
Advent Rebels
Cleanse and Renew: Although the tech description for this upgrade is fairly vague, it doesn't sound worth getting. It seems as though it gives allied ships bonus AM when you destroy an enemy colony. But by the time an enemy colony is destroyed, the enemy fleet has typically been beaten so the extra AM isn't really a benefit. It would be much better if this tech just granted a large and long lasting AM regen boost to allied ships at an enemy planet when said planet takes damage.
Aye, the problem primarily is that the short duration debuff occurring at a time when it's unlikely you face immediate battle just makes the tech way too circumstantial.
Either doing what you suggest or just flat out drastically increasing the duration would quickly make this useful- all it needs is for an advent Rebel player staying on the offensive to actually reliably have the buff during most battles. +75% AM regen is a huge benefit for any Advent fleet- it just needs to actually have that bonus while it's threatened.
Mass Communion: As pointed out in other thread, this tech just doesn't fit with the AR theme and is pretty much worthless as well. If it had no research prerequisites than it would actually save costs on media hub construction.
no complainst here
Vasari
Gravity Warhead: Change this so that it cannot target Titans, thanks Seleucia.
Yep this is way past due.
Bombers: I think every one agrees that their DPS per supply needs to be 30% lower in comparison to the other factions bombers*. Furthermore, it is their damage per shot that needs to be reduced in order to lower their DPS. Merely lowering their RoF won't help since they would still reach critical mass too easily and one-shot kill important ships.
If I could only choose one update to happen next patch this would be it. This is an inbalance that has been around through multiple iterations of the game.
Every other phase missile unit is balanced by having 24-30% lower base DPS per cost/supple as compared to the other races, yet vasari bombers for some reason actually do more DPS per cost/supply the TEC bombers. Phase missiles are a big deal- Vasari bombers need to lose 30% or so of their damage to balance that tool.
The defensive turret's Disruptive Nanites upgrade should not disable passive regen on Titans for 2 minutes*. That is just excessive. A 30 second debuff is enough.
Another minor oversight which is due for a revision. I'd be satisfied with either a shorter duration or just having it not disable titan AM regen(that is the real dealbreaker at present).
Phasic Trap needs reduced range, reduced duration and increased cool-down time.
Not sure I agree. phasic trap is one of the only vasari defensive advantages,a nd with the arrival of titans in rebellion is not as strong as it once was.
I'd say go with the other key vasari nerfs and see where they stand before hitting peripheral targets like Phasic trap.
Vasari Loyalists:
Vorastra:
Desperation: This shouldn't inflict splash damage on corvettes*. After initial skepticism, it became obvious that this needs to be nerfed.
Agreed
The Maw: (EDIT) No changes needed.
The only minor change I'd like to see to The MAw is have it changed to a proper channel. That way the Ankylon(and only the ankylon by the way) would be able to interrupt it with disruption matrix.
I think it is necessary if the Ankylon is ever going to be a viable support titan that relies on it's fleet for the Ankylon to have a countermeasure to The Maw. Making it interruptable by the only disable in the game that hits titans would give the TEC loyals this countermeasure.
Vasari Loyalists:
Kultorask: Only Gravity Pulse should effect enemy corvettes.
Correct me if I'm wrong but I believe Nanoleech already doesn't affect corvettes. As for Dissever- lots of titan level 6 abilities hit corvettes(The Maw & overcharged Explosive shot both do). Honestly I think it's fine for titan level 6 abilities to hit corvettes- the titan has to be fed to get to level 6, and that late in the game people usually have transitioned to carriers anyway.
Star Base Mobilisation: (EDIT) Make Orkies only capable of jumping between planets that have phase nodes*.
This would certainly remove just abouteverything overpowered about jumping orkies. Would also encourage the use of Marauders to use orkies offensively which I like.
All in all I like your changes. There are a few points personally I'd do differently, but by and large your vision for what needs to happen balance-wise is overall pretty similar to my own.
