I noticed two further little issues (maybe):
1.) Cylon Loyalist
Cylon Rebel can research "Are you Alive", "Procreation" and "Nanorobotic" to increase its population; but the Loyalist can't.
2.) Starbase-Upgrade-Hangar for Cylon
With the last Hangar-Upgrade you get 40 fighters or bombers.
Was that intended?
By the way the new models of Nep are awesome! And I really began to laugh when I saw the Yamamoto as Titan. The Yamamoto for the Pirates it's a really funny and good idea!
Ok, I was a little disappointed that you haven't chosen the Bismarck (joking)!