Flagship mod

This might not be possible as it would probably require some hard coding into the game. But it would be a good idea anyway.
I tried something similar with SEIV and it proved quite interesting. Basically turn on every minister on for your empire, so that the computer is playing 'you'. Then take 1 ship which you control exclusivly and see if you can make a difference. The only rule is you can only have one ship. If you need to upgrade you've got to scrap the ship and make a new one at the same planet.

Anyway the mod is this. Allow the creation of a flag-ship. This ship has a special 'captain' that gains better bonuses for experience. More ranks and with those ranks gets special bonuses such as, +1 movement, regeneration, generates supplies etc. The difficulty in making such a mod would be adding the ability for the captain to change ships. I suppose a special cargo, doesn't weigh anything, only one allowed in existence, only one allowed per ship.
Linking that cargo with experience would be very difficult, it's probably not possible. But it would be cool to have a flag-ship like this (or hero if you will)