So lets give this a shot... and don't be too displeased if I don't agree with you on all points. It's always good to have discussions.
All in all I had tons of fun playing this mod and will definitely keep playing it for a while... Let me know if you want some more feedback...
Well, this by far is the most important thing. What good is a mod if it's not fun 
Yeah I know, I haven't played the game in ages so I figured it was good to go against an easier foe just to get things started.
Hehe... well plague is played very well by the AI. The AI loves to spam cheap cruisers plus the capital ships are very tough. Allowing the plague to spread makes for very tough battles.
I had only the galactica capital there which just colonized it but I figured what the hell maybe I can delay them until my starbase is up so I went on to see what the old ladies got...
I'll get into stats more later. But the Galactica is pretty solid against normal capital ships. Though without knowing what Plague fleet you were up against that may have been foolish 
Bad mistake. The poor old lady didn't stand a chance. My weapons seemed to do only mild damage to the plague capital's shield while my hull was pretty roughed up after like 2 minutes (I noticed this even late in the game, the colonials don't match up well with the plague. Their weapons don't do that much damage and their hulls are faster down than the plague's shields most of the time with even numbers).
The plague probably has some of the highest regen rates on their hull and shields which I may need to look at again. However, the Galactica in reality is far stronger than say the Plague colonizer. Here's a quick stat comparison.
As you can see the Galactica's core stats are much better than the Plague's colonizer.
The thing with capital stats is they are misleading for the most part. That 66 KEW is the cumulative result of Front/Back/Left/Right.
The actual damage is:
KEW: 15/13.75/18.75/18.75
Missile: 17.85/0/17.85/17.85
Autocannon: 0/0/10.5/10.5
# of targets per bank is 1/1/2/2
This makes the total damage output potential a whopping 234 DPS which far exceeds the plagues 51 DPS.
The thing is though to realize this DPS you need to position the Galactica between the enemy to get all banks firing otherwise you only using 1/4 of the total output potential.
At some point I figured I had him outnumbered with capitals, asgard battlestars and repair flattops, and from here on out it went pretty well, even tho I think it was only because of numbers as I still had the impression my weapons weren't doing a lot of damage.
The Plague fleet are mostly forward firing units making them very tough in a stand off. The key is to position your superior units to bring all your guns to bear. Though the plague can and will use it's capital abilities which right now are vastly superior to the Colonial stubbed out abilities.
One thing that really bugged me alot (and not because I've lost the ship) is the Galactica's weak armor and lack of hull points. I don't know about the Nova or Thor class, but she definitely needs to have better armor and hull than the Pegasus or Valkyrie.
Maybe you feel this way, but the Galactica's armor is 13! That is hardly on the week side. With even the vanilla research this can be pussed even higher. The Galactica is by no means superior to the Pegasus or Valkyrie which are more advanced Battlestars. Where I will agree is the Valkyrie's stats are much higher than I intended and will be reduced to show the smaller scale.
The Valkyrie was a much older and smaller ship and in the series served mainly as a reconaissance Battlestar.
This isn't true. It was a demotion for Adama to be assigned to the Galactica.
"Interestingly, the story of Ragnarok parallels with the career of William Adama, the former commander of Valkyrie. Adama, considered a fallen hero by the admiralty, is transferred from the advanced Valkyrie to command the aging Galactica about a year before the Cylon attack. Later, with the fall of the Colonies, he finds himself in the Battle of Ragnar Anchorage, the last battle within Colonial space."
The Valkyrie is a smaller Battlestar true, mainly because it's more advanced systems allows for a smaller design requiring less personal to manage.
And for the Pegasus: Remember Season 3 Exodus Part 2? Where the Pegasus got destroyed? The Galactica lasted much much longer in that fight, already having taken a lot of damage by the Cylons before the Pegasus jumped in to help out. Plus the Galactica had already sustained heavy damage when the fight started from falling through the atmosphere of the planet and then jumping into orbit before hitting the ground. I think it was even said somewhere in the series that they built them tougher in the past.
This seems to be more to support a plot line than a real representation as to how the Battlestars were constructed.
The Pegasus definitely needs better ship to ship weapons than the Galactica and do more damage there, but the latter needs more fighters (older ones) and a lot more hull than the Pegasus.
From what I can tell the Galactica is not capable of carrying more fighters and raptors than the Mercury class Battlestar. Additionally the Mercury class specifically mentions it has built in production facilities for Mark VII vipers.
"Pegasus also has Viper Mark VII production facilities, allowing the ship to re-arm itself on extended deployments, provided the battlestar has access to raw materials such as ore"
Another point I leave the timeline intentionally vague. There is no reason to assume the Galactica has more Viper MkII than MkVII's. The Galactica at it's decomissioning launched MKVII's to defend itself and only launched the MkII's after it lost it's original MkVII squads. Given I can't detail how many of each squad type is allowed I've left it to the player to decide how many squads of vipers or raptors to build out and of which type.
The Colonial fighters need to be more tough. Even when I had my opponent outnumbered they fell like flies. Battlestars are more like Star Wars ships that rely heavily on fighter support and let them do the work while the carrier ship stands a little back and tries to hold it's own against the ongoing attack (They're built for that: Tough hull with a lot of AAA to intercept missiles and enemy fighters). I think the PDS you incorporated is the right way to go in that regard, but the Battlestars themselves, IMO, need to be somewhat more tough as well as the fighters.
Well, the show definitely depicts a scenario of only battlestar/strikecraft, but I'm using other sources such as Wolf's shipyard to build out the mod. In this scenario a Battlestar did not engage enemies by itself but instead works with Gunstars, Escortstars, etc to build a formidable fleet. I also like making sure capital ships are tough but there is risk of losing it when you engage in battles.
What I'm trying to do is bridge this gap by having SO many of the ships contain strikecraft. The Gunstar Alberio (LRF), Escortstar Berzerk (AA), Asgard (Heavy), Sentinal (Carrier) all are able to field strikecraft which is a huge deviation from vanilla sins.
-The Plague's starbases seemed a little weak. Might be because the Medium AI didn't finish upgrading them, but compared to their ships they were pretty easy to bring down.
Yep, the colonial battlestars would be tougher than a low level starbase. A starbase's advantage is the 4 targets per bank making it deadly against larger fleets.
A little note on balance... People asked for the mod to be released which I was cool with doing. But it's obviously not complete from a balance perspective as I'm trying to get a good feel from basic stats to strategies. Other things like abilities are more rough sketched and the research tree is not tailored to Colonials. I think a lot of your frustration will be resolved by a research tree geared towards the colonials that allows the battlestars to be a powerhouse late game but not overwhelming in the early game. By example I want to add research towards the higher tiers that adds additional targets per bank to capital ships and completely change how the hull/armor/PDS upgrades work.
