Well, I has been experimenting a lot with the fight and I would like to throw out a few thought and things that I done. Since it may be a lot of change I made so I hope you won't get angry and thinking I am telling you what to do with the mods, at best treat these as suggestion and please know that I fully respect and enjoy the mod.
The majority of my times had been spent playing the Alliance, and I notice IMO, many odds things. They are mostly game balance and such.
- Shield Restore: this is a capital ship grade ability, and for good reason. Giving a Cruiser this ability is really overpower IMO. Anything backed with 3 or more of these guys is basically immortal. It's one of the most useful ability I remember when playing as TEC, but due to it's mounted on a CapShip I can't spam it less I want my firepower suffer, it's not the case here. IMO no capship ability should be given to anything beside a capship, especially an ability that can be stack "indifitely" like this one. If you still want to maintain the idea of a shield frigate, then Shield Regeneration might be a better choice since it has a limit to how many you can stack. Although I prefer give it a repair ability or the advent's shiled bubble. Once I had 5 of these cruisers backing up a starbase against a gigantic AI fleet with probably a couple dozen Dreadnaught, the battle went on for like 15 min, when the dust settle the startbase does not even lose more than 1000 shield point.
- Capital Ship Usage: when I look at the files, I don't know why I would want to use the MC80 once I have the Maria. The samething can almost be said about the MC80a and the Liberty except the one saving grace of NanoniteRepair ... which actually not that important, seeing how Alliance ships have a lot of shield and the Shield Frigate work so much better. This pretty much render the two early capship obsoleted. Statwise it might be that case according to lore, but I think game balance also importnat. The 3 original races pretty much have a place in the fleet for every ships. So I did a major shakedown for the alliance ships, and I think it worked pretty well. This is not saying I'm disregarding the lore side of the story, I did try to adjust to it.
+ MC80: Flakburst/AntimaterDetonate/AdaptiveShielding/LastStand. I increased shielding by 100, also I increase the gun banks so that the ship have an "all rounded" cover (except the back). The total laser value for F/L/R/B are 45/30/30/0. This way I find that the MC80 still justify its use in the fleet even after the Maria is available.
+ MC80a: ShieldRestore/EMP-Charge/Colonization/ReduceAbilityCost. As you can see I turn this ship into a combat support roll, and its existence is pretty much guarantee in the fleet. I keep everything else the same except reduce the total number of squadon (at level 10) by 2.
+ Maria: Taunt/Powersurge/EnergyAbsord/LastStand. I reduce the value of its Right and Left laser while keep its frontal value the same. This way the ship stands true as a front line ships. Soak up the damage and attack the enemy head on. No matter what this ship probably have the most present in a fleet, that's why I gave it Laststand which I think more approriate then CeaseFire.
+ Liberty: BattleMeditation/Targetuplink/IronBlast/CeaseFire. This is an interesting ship and I tried to think of a way to justify it. First, I bet many associate it with a command ship, so it definitely has to be powerful - but that is in term of story - in a game it also need to balance in a way that it won't be spam. I'm pretty happy with its fire power so I left that alone as well as its hangar space. The solution I come up with is the above ability line up. Giving it two "non-stackable-fleetwise" ability will make it in-effective to have more than one in a fleet. Also ... well, the idea of Ceasefire on a command ship just seem to make more sense than on a front like ship. And BattleMeditation ... common, that ability just screams StarWar pick me in your face. Bastila anyone? 
That's about the capital ship shake up, as I said the main reason I'm doing that because I want to maintain a decree of usage of all ships through out the entire game. I also playing with the Frigate and Cruiser a bit although nothing concrete yet. But I'm looking at stuffs like "StealAntimatter", "GiveAntimatter" ...etc... because they seem to make sense with the lore.