We're adding carriers to fill that role. As opposed to Inferno, our conception of the carrier is a big, fast, lightly-armed box exclusively for carrying fighters. Capital ships are only used in rare instances.
As far as making a separate fleet for each solar faction in chapter 1, that'd be pretty much impossible from where we stand now. It took us a full year to scrounge up enough ships for one faction; unless we get a modeller willing to churn out Terran fighters like hotcakes, we'll be using the same ships for every faction.