HerrPinguin, I could quote parts of your last post, but everything you said is pretty much dead on 
We are running into the stage where the capital ships can't be balanced much more because abilities aren't the only things that need to be addressed...and this, unfortunately, is where we are going to start running into major problems...
Pretty much everyone agrees that Scramble Bombers is OP...but even with that majority opinion, exactly how to change that ability was not easy...
We can all recognize that Gauss Rail Gun needs to be fixed, but there are so many different thoughts on this ability...and in the grand scheme of things GRG is a pretty straight forward ability since we're mostly just tweaking the numbers...
Now take something like Animosity...or Clairvoyance...or Subversion...and suddenly it becomes pretty much near to impossible to reach any sort of consensus...two or three people might agree on an idea, and everyone else might say "Well, it's not the best but I can live with it"...that is likely a best case scenario...
Now, extend this to things beyond capital ship abilities...how do we make capital ships more resilient? Some people don't think they even need to be buffed at all...some want to focus on LRFs or bombers...some want to buff the damage, or HP, or shield mitigation of all the caps...there are ideas on boosting their speeds, number of weapon banks, and the list goes on...
If we were to try and fix LRFs and bombers, how would we do it? For LRFs you have armor type, speed, DPS...with bombers you have HP, damage, armor type, hull regeneration, DPS of fighters and flak, damage types of fighters and flak...and both of these issues also involve phase missiles...should they be nerfed? Should they be left the same? Should they bypass less shields but do more raw damage? The list goes on...
We are coming to the point where people may have very different philosophical views on what direction the game should be taken...and this is going to make consensus very difficult...in addition, it will pretty much eliminate any chance of this mod being widely adapted...game balance is one thing, but going through every element of the game to encourage diversity of strategy while maintaining (or improving) balance is very different...it isn't just balancing the game, its evolving it...this isn't inherently a bad thing, but it's important we don't kid ourselves in what we're doing...
This is going to be a long post, so bear with me....
First, lets categorize the capital ship abilities into priority levels:
Level 1 - These abilities need to be reworked and undergo major changes at the conceptual level
- Animosity
- Guidance
- Clairvoyance
- Colonize (Jarrasul)
Level 2 - These abilities need some significant balancing, but conceptually are fine
- Gauss Rail Gun
- Shield Restore
- Magnetize
- Incendiary Shells
- Scramble Bombers
- Subversion
- Phase Missile Swarm
Level 3 - These abilities may need some small tweaking but are more or less fine
- Flak Burst
- Adaptive Forcefield
- Finest Hour
- Missile Batteries
- Heavy Strikecraft
- EMP
- Missile Barrage
- Energy Absorption
- Cleansing Brilliance
- Vertigo
- Vengeance
- Domination
- Provoke Hysteria
- Distort Gravity
- Phase Out Hull
- Assault Specialization
Level 4 - These abilities are already fine and probably don't require any work
- Embargo
- Rapid Manufacturing
- Colonize (Akkan)
- Ion Bolt
- Targeting Uplink
- Armistice
- Flux Field
- Radiation Bomb
- Raze Planet
- Detonate Antimatter
- Telekinetic Push
- Adept Drone Anima
- Energy Aura
- Anima Tempest
- Colonize (Progenitor)
- Malice
- Shield Regeneration
- Resurrection
- Concentration Aura
- Reverie
- Power Surge
- Jam Weapons
- Disruptive Strikes
- Volatile Nanites
- Repair Cloud
- Microphasing Aura
- Replicate Forces
- Gravity Warhead
- Nano-Disassembler
- Drain Planet
- Stabilize Phase Space
- Deploy Siege Platform
- Disintegration
As you can see, a very good portion of the abilities need little or no work...but some of them need a lot of work...
Here is another list of things that may need to be addressed...these are thing just off the top of my head, and I'm sure everyone has things I haven't thought of to add to this list...I have tried to include things I don't necessarily think are an issue but others do...keep in mind that not all these things need to be changed, but all may need to be considered in order to get the desired effect:
- Capital Ships - DPS, # of weapon banks, HP, shield mitigation, speed
- LRFs - DPS, spead, stats of anti-medium weaponry
- Bombers - DPS, stats of anti-very heavy weaponry, hull regeneration, HP, DPS of fighters and flak, stats of anti-light weaponry (for fighters vs bombers), construction rate
- Phase Missiles - shield bypass, weapon types of ships like sentinels and Vasari fighters, power against Capital ships
- Phasic Trap - Duration, cooldown, antimatter cost, range
- Distortion Field - Cooldown, antimatter cost, duration, range of debuff
- Scouts - DPS, particularly against LRFs
- Cielo Command Cruiser - Designate Target, Embolden
- Illuminator - DPS, ratio of frontal to side DPS
- Skirmishers - DPS, may need a buff depending on how/if LRFs are weakened
- Deliverance engine - Duration, more secondary buffs, cooldown
- Kostura - Duration, damage to structures, damage to ships
- TEC late game power - God knows what, but TEC needs it
- Advent early game power - Depends on how Vasari/TEC are affected, may or may not need to be addressed
- PIRATES - Definitely needs some work (DesConnor I promise I'll look at your mod sometime)
- Refineries - Increased productivity of refinery ships, reduce cost
- Resource Focus - higher bonus, maybe needs a conceptual change
- Colony Pods - needs to be more economical (at least to the point where it's worth considering)...
- Induced Reverence - needs to be more economical
- Repair Maw - I've hear mixed things on this, may or may not need to be looked at
- Rarely used technology - Communal labor and several others
- Pacts and Envoy bonuses - may need some balancing, Vasari/TEC packs are very strong while Advent packs are somewhat weaker
Oh my...I'm sure I forgot some things, but the point is, there's a lot to be addressed...
Since we are at the point where philosophy on how the game should be is likely to disrupt any chance of consensus from here on out, how to proceed needs to be addressed...
There are A LOT of areas that need to be looked at and improved...a lot of people are very interested in being involved in such changes, but unfortunately the focus has been on capital ships for a long time and I think some people have been turned off by this...I know there are lots of ideas out there for other things...therefore, I encourage others to start discussions on the changes they want to see...
Some things are entirely independent of other items on the list...refineries, pirates, useless technologies, super weapons...all those things could be worked on and be entirely independent of how the capital ships are changed...I'm going to see this through to the end, and if I'm the only person making changes or using this mod, then so be it...yet, there's no reason for others to not start their own discussions if they don't feel like waiting for this thread to move on...
If this is going to be a community effort, I think several areas need to start being addressed now instead of just one area...people who aren't interested in capital ships yet interesting in changing other areas should start those discussions...this can be a community effort, this can be the work of a few individuals, or this can be several works by several individuals or groups...but it depends on what everyone else is willing to do...
Right now there is about 5-6 people (that I know of) that have been focusing and testing the capital ship changes...I want to thank all of you for your ideas and willingness to test...