I hope that major changes will be forthcoming in this aspect of the game. The commander ships are way too powerful and make it pointless to do much in the area of combat ship development until much later in the game. These ships shouldn't be available until you have the technology and ability to build them. I would like to think that this is a science fiction game, not fantasy.
To me, it would also make more sense to make them fleet commanders and perhaps only let them get the affect all ships in the fleet type upgrades..