I thought I would mention a bit of cheese I use on the AI when I'm at war. Others can try it out if they want, but I'm mainly hoping that exposing areas of weakness like this will eventually lead to a stronger AI in the future.
Basically I leave my core worlds that are deep in my territory unprotected on purpose. The AI sees this through espionage so it doesn't matter that they are far out of their sensor range. The AI will unfailingly send small groups of transports to the planets not realizing that I have groups of fast fleets waiting to pick them off. Yes, the AI has gotten better at escorting their transports, but it can just as easily be exploited this way as well.
-Transports generally slow down the fleets making them easy to catch before they reach their destination.
-Transports take up logistics of the fleet making the fleets weaker in general.
-Every transport destroyed in space is 1b less people to kill on their planets which lightens the burden of invasion.
-The enemy's economy is similarly hurt by the loss of tax payers.
-Much of the enemy's production is tied up making these ships which end up as bantha fodder.
As far as suggestions to get around this, I can think of a few, but hopefully some feedback about this will get some more ideas / brainstorming on 'fixing' this weakness.
-The AI should upgrade their transports as well (or more often) when new engine techs become available.
-Instead of making fleets with transports the AI could simply keep fleets on top of them (like I do). This protects the transports while keeping logistics free as any attacking fleet gets to fight the most powerful on that square first.
-Maybe the AI could evaluate fleet asignments deep in enemy territory or farther away as more dangerous and focus on them less rather than thinking that any unguarded planet is easy prey.