Currently when a flagship is built it starts with auto-fill on and immediately steals whatever defense ships are in the system, often resulting in a hodgepodge of ships. I suggest firstly that there be an option setting which can toggle whether a flagship starts with auto-fill.
Secondly, it would be wonderful if we could create and store fleet templates. Something that could easily be selected and would fill a fleet with the right percentage of designs. For example, I would create a fleet template with 40% design A, 20% design B, and 40% design C, and it would automatically create a fleet with the proportional numbers of ships. This would be easy to apply and would easily scale based on the flagship support limits. It would add a lot to the game, I feel.
It wouldn't hurt to allow us to set one of these fleet templates as the default for our planetary defense ships, either. Right now it's very difficult to control what ships your planets choose to use to defend themselves.