I think the intent, haha, like i know, which i dont, but im taking my impression here, okie, but i think the intention "might" have been to find some way not to spam the caps, since they are very powerful. And to have people concentrate on the frigates as their mainstay for the bulk of their fleets, with caps sort of icing on the cake so to speak, powerful and buffed (with abilities) as support ships as well.
But to be honest, i love the caps!! Haha, who doesnt? And i think it would have been nice to have the user decide what to do, but perhaps given half a chance we would all concentrate on the caps.
Personally, and this is just an opinion, but i think it would have been nice, as you say to simply have all the ships available as "levelable". I guess what that would have done is make them all caps. And to simply have them cost different amounts based on perhaps strength or ability.
Anyway, just my thoughts, but i agree, it would be nice to find some alternative to the way it was originally set up. Just because i think different people have different play styles and preferences. And this way they get to play the game the way they like it. 
Take care,
-Teal