Basically I think that since space is vast, and ships are a gajillion miles apart, tiny shuttles are contrary to logic. Just my feelings.
Of course, this means that in my house, Akira is not a through-deck carrier. Not sure where that idea comes from, but I think it is pure speculation.
It also means that I have to figure something out for the Coronados because I like them as a specialty ship. OK... shuttle carrier, but not a fighter carrier. I can see a role for a ship that carries a lot of shuttles, sort of like seaplane carriers in World War II.
And note... I do not consider ships like the Peregrin as shuttle type fighters. Rather, they are small interstellar-capable ships, just like runabouts.