Back to topic.
I like the idea of a flagship that allows for an upgrade for the fleet.
The downside is this vessel will be targeted more often than not and will die quickly.
Let the flagship have a higher shield mitigation to stop focus fire on it from working aswell. Sheild mitigation is teh reason you dont make entire fleets focus fire one target at a time because it becomes inefficient as the more focusfire=more shield mitigation=less damage.
Maybee the flagship should be like your home planet upgrade? Losing the home planet is a big thing because it is the conter of your alliegance and has a bonus tax income. If you can move your home planet then surly you can change your flagship and make new ones the same way.
I think a flagship should come with buff abilitys that can take effect from just the local gravity well to your entire empire.
Also each different kind of capital ship being made your flagship has its own abilitys. So a marza will have a different abilitys than a kol.
Exsperience for your flagship should be kept seperate from the exsperience for the capitalship. So to go to level 2 the flagship must get 2000 ex or something which is not shared like the exsperience for the capitalships. So for example each scout ship gives 5 capitalship exsperience, which is divided up beetween the capitalships. It also has 5 flagship exsperience which is only given to the flagship for its flagship upgrade.
Also to stop flagship destructions from being a total waste of time and energy for a player if someone focusfires it down. The next flagship they assighn should have the highest flagship level obtained-1 level, as their starting level forthe flagship abilitys. That way if you get a flagship to level 6 and it gets killed, the next flagship will start at level 5. If it gets killed before reaching level 6, the next one will still be level 5. If the next one gets to level 7 and dies, the next one will spawn at level 6 and so on.
A flagship should maybee not have any special abilitys, other than the extra health and firepower. To gain more abilitys a sperate research tree might be needed, just like the starbases have. So maybee you could research an ability for a carrier flagship that takes place at level 6 which increases all merchant ship speeds by 10% increasing their income by 10% aswell. An ability for a kol at level 9 would be for all capships in the same gravwell to be given an additional wepon bank that would be a flak gun that helps shoot down enemy fighters. A level 10 ability for all cap ships to save that level 10 if they are killed and not go down a level.
Just some ideas that I had that could be added to the pot.