I think the devs probably wanted the players to have something special, like a single real flagship, that would be more of a symbol than actual firepower.
When they let people capture them and accumulate more than one, the "specialness" went away, and that's what I meant by saying the system needed reworking.
OFC if they want to add more ships in the game, then the MOW needs to lose it's value, and become more of a liability(which it already is) than asset.