Had a fleet of transports stacked on top of a fleet of warships, believing the warships would be targeted first. They were not. This seems silly.
Hey, transport ships take a lot of logistic slots for a reason. Protecting them is a task in itself, and if stacking ships on top of each other worked, then logistics would make much less sense in the first place. You have to add ships to your transport, or it will be sniped by AI a lot. It's also somewhat of a comeback feature, because it forces the player, who is attacking, to have somewhat weaker fleets (those with transport), which may be an optimal target for the other side, which is already loosing. But if no protection to transports is provided they will be snipped, and at least your advance in planet capture stalled.
Given the fact that combat is fleet-based, I don't really see the validity of your explanation. Transports add nothing to a fleet, already putting you at a disadvantage in fleet on fleet combat. Then you have the fact that there's no zone of control exerted by fleets- so even if you create screener fleets for your fleet loaded with both combat ships and transports, the enemy can just zig straight through them to get at the weakest fleet. Given the massive move advantage in their own territory, the entire gameplay logic falls apart. Further, it simply makes no actual sense for a transport fleet to be the one attacked first when an enemy attacks a hex you occupy. It's so counter-intuitive that I actually was shocked after a year of playing to see it happen. Why would two fleets sitting next to each other choose to intercept an attacking force with the defenseless fleet? Don't take my disagreement with not valuing your response, I just don't think it's valid.
Addendum- maybe zone of control should be a thing for fleets with large enough hull types.
IRL the transports wouldn't engage with the enemy. In space you can see the enemy advancing at great distances. Either the escorts would advance to engage leaving the transports in the "rear", or the entire fleet would turn tail and try to flee if the fleet commander determined it would be a losing battle. That said, if the attacking fleet was faster than the defending fleet, they might be able to catch the defenders before they can do either, and if they are trying to flee then they should not be engageable in the month of the first attack, but on the subsequent turn they would not be able to able to disengage. I hope that's clear even if it is a little convoluted.
There is a bit of a design flaw where the default transport is not designed to be in combat at all, but need to be in a fleet (and combat) to be protected.
Just don't use the default transports. You can throw the same module on a medium hull and give it weapons and defenses. The +range one tends not to be targeted.
Now it can merrily join your fleets and contribute to the fight.
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