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When you create a fleet led by a capitol ship that ship is designated as a flagship in its info card. However I've noticed that late game, when I have several high level capitol ships in a fleet that none of them have a Flagship designation.
What exactly causes a ship to be designated a Flagship and why is this not happening at the end of a game.
as far as I know, your first capital ship - the one you get for free - is designated flagship. it's the only one and if destroyed, you cannot get another one. and there is no bonus or any other gameplay impact, it's purely aesthetical. at least I'm pretty sure of it.
It is based on exp. level not points level if you only have one level ten ship that is the flagship. If you have two level ten then there are no flagships. I know its dumb
The "Flagship" designation is only given to the highest level capital ship in your fleet, regardless of when it was built (1st, 2nd, or 10th). No capital will have this designation if there are two (or more) capitals with the same level and they are all the highest leveled capitals.
In the Empire Tree, if my memory is accurate, the caps are sorted by level, then order of construction. If you had all level 7 capitals, for instance, they would be sorted in order they were built from oldest to newest when they're all in the same gravity well.
You should be able to designate a flagship for some kind of fleet bonus. Maybe even just a significantly higher culture repel rate, or some empire specific bonus. Obviously it would have to be your highest ranking ship, and some kind of limit to keep you from changing it several times if you have several top level ships.
What are you talking about? Whatever ship you have selected during "create fleet" will be the flagship.
I never even noticed this before! 
But you are correct, there should be some sort of bonus applied to it's fleets abilities.
This has been complained about numerous times...(mostly by me) and by others.
This happens because two or more ships have the highest level. whichever ship that is highest in your empire's fleet is termed the flagship.
edit: nevermind, didn't see the post above
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