This question came up on the 6/12/2015 dev live stream. I wanted to give some feedback since it was not clear how this worked.
If I attack a hex that has a stack of ships/fleets on the galaxy map, it seems to automatically attack the strongest ship/fleet in that stack. There is no way to attack a weaker ship/fleet if I want to. Cycling through the enemy fleets and placing another on the top of the stack does not effect this. The only option I have is to attack the strongest ship/fleet.
The AI on the other hand can attack whatever ship/fleet it wants in a stack. This has frequently happened to me where I have a fleet on transports and a fleet of capital ships in the same hex, and the AI just comes in and wipes out my transports with a tiny fighter.
IMO, this needs to be fixed. Either everyone can select which ship/fleet in a stack it wants to attack, or the AI should have this ability taken away. Probably the easiest thing to do is to allow a player who attacks a stacked hex to automatically attack whichever fleet is showing on the game map. (ie you can click on the stack until the fleet/ship you want to attack is on top of the stack.) This way the AI programming does not have to be changed with how it already works.
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And before you say just put the transports in a fleet with other ships to protect it, this will not work well. If the enemy fleet is 6 attack ships, and I have 6 defense ships of roughly equivalent strength, and 6 transports, I am not going to split the defense ships between 2 fleets.
The issue I see is that the AI can select which ship/fleet it wants to attack and the players cannot.