Honestly, why do you buff up anything now ? That dont make any sense.
So far i understood you want a primary Cap-fight anyway. And so far i know there arn't any fighting vessels beside the battlestars at BSG. Just remove all Frigs beside Scout (Raptor) and all Cruisers beside 1-2 Logistic/repair. Add instead some different Strikecrafts.
You should reset all values. Because the base entrenchment stats was good balanced. It dont make a differnce when you got 100000HP and your weapons do 100 damage (example), its the same like they are 10000 HP and 10 Dam or 1000HP and 1 Dam.
And since you said you want buff the non Cap ship too, you buffed all ships, so its time to go back to the old values.
Ok you don't want any shield, thats ok, raise the Base armor by 50%.instead. Maybe reduce the Powerup from levelups a bit, so far i remember my Colonial Galactica Battlestar got 49 Armor at lvl 10. Ok the Weapon damage went up too so at closefight with other Cap's they need it. But i still think reduce the powerups by 50%
If you want a bigger use of support cruiser reduce the HP regen value of Caps, so they need repair ships.
Look at the Starbases too.
All bases use Beam,missiles and cannons.
Colonial bases just should use Cannons, Cylon just Missiles like their Cap's do.
Adjust their abilitys more, Self destruct fit better to Cylons, and Meteor control dont fit to Cylons
I think Vasari base fit better for Cylons anyway.
But thats all just suggestions, let us surprise with a new 0.5