Hi there, I'm new to this site, but I did do a search first and didn't see a thread on this topic already, so I hope this is the right place and correct way to make this kind of post.

None of the AI opponents you play against during the game has any idea how to do the academy quest or how it works at even a basic level. Bizarrely, the unknown civilization pirates that are spawned to oppose the player knows exactly how the Academy Quest is supposed to go, and goes after it single-mindedly.

In my experience the things that the AI will do, is they will take their explorer class ships, and fly them over to the objective points, but I've never seen them actually assign a hero to them, or use the big hero fleets they are flying around to go capture an objective point. They will also, even if you are on the same team, close their borders to you and complain endlessly (do we like puns?) about you having your ships in their airspace. 

Pro tip, if you have to capture 2 or more objectives in the same enemy or alliance's airspace (spacespace?) then you better send two different hero led fleets in there at the exact same time, because closed borders doesn't kick you out, it just doesn't let you move around or enter, so get those heros on those planets and just hope for the best, because Horatio simultaneously doesn't understand why you are uglying up the planet that just appeared beside him, but he is going to continue to fly an Explorer over to the other side of space and use it to keep your other hero fleet company... and then leave it there for the rest of the game because he forgot why he did that in the first place.

Is this everyone's experience? I have seen a few other recurring themes regarding the AI popping up as well, but I didn't want to split the focus of the thread too much. AI aren't so great at pirates still. I had a lair in enemy territory last until roughly turn 160 in my last game. They also don't seem to buy ships from the market place, and rarely sell them. Some mysterious pirates or something occassionally sell awesome ships early game like the "Sword", but I don't see AI putting ships or materials up with a lot of regularity, even if they have a massive amount of Strategic Resources compared to the Dust on hand I see them having when I go to negotiate with them, they seem to like to hold on to 99% of their resources no matter what.

Like I said, I'm mostly concerned about how poorly and strangely they handle the Academy Quest in this thread at least. Does this sort of thing happen to everyone, or just me?

I've had similar experiences regarding AI behavior and the quest. It does send scout ships in the first phase but doesn't really manage the second one. One weird exception on one occasion I've seen is the Vodyani AI throwing its Arks to Lodestone systems, but that doesn't help the actual quest objective that requires heroes. Regardless the worst part is that the AI seems to randomly pick a side but doesn't change its behavior to suit the quest: an allied AI who is in opposing side of the quest will stay friendly and forces you to break the alliance, whereas cold war foes will stay hostile even if you're on the same side with them forcing you to declare war rather than cooperate, especially if they closed borders.

Another issue is that the second part of the quest doesn't end when you capture over half the systems as either side, meaning the winning side has to capture every single system even when you're at the point that the losing side can't win anymore. The quest itself also triggers way too late in comparison to victory conditions so there's really no reason to drop whatever you're currently doing to participate in the quest, assuming the quest even manages to trigger in the first place due to an early victory, though that's probably more of an issue with victory conditions in general considering the max turn limit on default speed is 300 yet nearly all my games end well before turn 150.

I discussed this with a dev few months ago on the quests / event feedback thread so they're at least aware of the issues, and one possible suggested solution to Academy quest and diplomacy was to turn the Lodestone systems into no-man's land where you can attack the opposing side regardless of regular diplomatic relations. The quest properly ending when half the systems are captured is supposedly in the development backlog as well.

One more thing is that both sides of the quest have the exact same rewards, making you question what is even the point of choosing one side over another in the first place, especially because the AI picks randomly as well. According to devs it's for balance reasons and because the first part doesn't communicate the eventual reward (however that sort of message shouldn't be hard to implement).

I've made a privateer fleet to remove my allies from the lodestones before, but that's difficult because it requires there actually be ships up on the marketplace, or that you still have the ones you bought at the beginning of the game.

Good to hear that the Devs are probably aware of the issue though.

Yeah, the academy quest has some flaws, it may work in multiplayer, but I'm not sure I really like the way its designed right now, especially with the AI. The AI doesn't really know how to assign heroes to fleets specifically to complete this quest, so if you don't do it, the quest stagnates at the end. Then, completing the quest yourself requires sacrificing the use of one or more of your heroes for a very long time in the game, which isn't always a great idea, considering your fleets are often wanting to be active in wars and other quests.

So, the majority of the time I play the game, the quest just sits there at the end stage for a long time, without getting completed. I think the quest would be better without the hero requirement, and if the AI prioritized it more. Ideally, epic wars should be fought over these spots, but right now, its basically, "Ugh, my ally has an explorer on this spot, better waste my hero and hire a mercenary to clear it out, then sit there for a whole bunch of turns until its completed before moving on to the next one."