Well, I've been experimenting with AC3D and the Object Editor on stuff like the Tower and Maproom (thanks again for the assistance, BlauK). Haven't actually tried any of my modifications in game, but I've made a completely new Tower and Maproom that ARE recognized by the terrain editor (note: COMPLETELY new, well, except for elements I borrowed from the default models, but at least not replacing the existing shapes so they're as good as new).
I wonder if it's possible to do the same with a ship. Say, take the CV, rip out its hangar, find the important bits in object properties, and build a new shape around it (something like a CIC) and put it into the cruiser model and rename it something like, CA2 or something to differentiate it from the default cruiser. Then just set its type to be a ship when you load it in the TE. The only thing that's technically changed on it is the addition of the hangar (maybe the tower, too, mocked up like the ship's bridge).
Now, one problem I forsee is that it'd probably still be called a "C" group, so there'd be some confusion unless you knew already that "C# is a cruiser."
Could probably have like, one special cruiser as the "command ship," with a second normal cruiser and a couple destroyers. It'd add a TON of flexibility for guys who like blowing watermelon up with big guns, plus, it'd allow the CV groups to stay a safe distance away from the target, and still have the firepower to pummel the enemy into submission by sending in the cruiser and tin cans to bombard bases (#2 reason I've noticed for bringing the CV groups right up to a base is for the firewpower).