No matter how "cost effective" small ships are in the short run, your CAP ships seem to cost less in the medium and long run. This in turn makes researching new ship types fairly pointless...
Maybe I am missing something, but building all CAP ships seems too effective, at least against the computer, and the only way I can win on the hardest setting.
Maybe it works against the mindless computer...but try building a capital ships only fleet in the online multiplayer game (against halfway decent players) and watch what happens...
If you build a fleet of 12 capital ships (600 supply points) I could build a fleet of 100 Illuminators (100 x 6 supply points = 600). Those 100 Illuminators will then focus fire on the capital ships and take them down one by one. Watching capital ships explode is one of the more satisfying aspects of this game.
Now, it might make sense to take the 600 supply points and build a Progenitor Mothership (with shield restore) (50 pts) and a Halcyon Carrier (increase rate of weapons fire and hence damage for the fleet) (50 pts) and then build 83 Illuminators (498 pts). This fleet will pwn 12 capital ships, too.
After you get comfortable with the game, come play it online. You'll enjoy more intense games (since you face the prospect of actually losing) and you'll get to enjoy chatting with other players and using teamwork and having teammates, etc. Just click the Ironclad Online buttom and set up an account.