Hey I've got a suggestion for the MOD. Make the capital ships cruisers, all of them except the sovereign, neghvar, dderdix and enslaver, those would be the only buidable cap ships and the strongest of all in the fleet. My reasoning for this is two fold: one it forces the AI to build more of people favorite ships and would help to solve the problem of all of your cap ships in a battle being targeted first. With just one cap ship the AI doesn't seem to focus all of it's attacking fleets attention to it, thus it would survive longer without needing to be uber'd up. Of course if you roll into battle with a bunch of sovereign's then it's not much of a change.
Anyway I came to this conclusion after "tweaking" Stress and Shimmers mod a little bit (I won't spread it and respect the authors rights). I started by combining my favorite Romulan, Federation and klingon ships into the Fed race, a total of 27 ships with 9 frigates, 9 cruiser and 9 cap ships. i played against the Dominion like that for while and then turned the Borg on and made them a playable faction. What i realized when I turned on the Borg is that the AI doesn't want to build unless they have at least one Cap ship, so I gave them one just so they would expand and expand they did! They built several of the single cap ship i gave them and they also built all of the frigates and cruisers (except the coffin for some reason). next I decided to experiment with the Fed's and klink's. I gave them each just one cap ship and the same thing happened. The problem I keep running into is i still haven't figured out how to make the cap ships in the game cruisers, still looking through all the files to figure out what needs to be edited. but what I'm getting at is you could make the cap ships cruisers and move them into the frigate factory, there can be a max of 9 slots so that would absorb the extra ships.
The last reason for my idea is the AI usually only builds a couple different types of cap ships. Sometimes it will build all of them (mayabe) but generally just one of each. So this would throw a little more variety into the mix.
Ok so in closing I just want to say that this is a suggestion only and not a complaint. The game plays great the way you guys made it and if I or anyone else is just not satisfied then i guess I'll just have to learn to MOD myself! Thanks for the game guys.