I'm sorry if this topic was already asked before.

I played 200 hours, but I still don't know if there any others penalties for loosing Academies quest besides blocking a way to hire new heroes. Because if it's the only one, I have a few questions.

How Academy suppose to feel?

Academy is big thing. We have a fev quest (produce most of the dust/science/food etc.),  during which we got only pieces of story, and all we can do is only guess what's Isyander hiding from us.  We have a Celestial Worlds DLC, that told us how Academy work behind the scenes and how complicated it is. And then, the moment of truth. Main quest. No time for caution. Final battle. Moment, that well decide the future of galaxy. But...should we care? On losing quests we get a reminder, that we falling behind in progress, and that we can't get a full story. If we fail in battle for bringing The Lost back, we lost only new heroes. Game still beatable from there, for the sake of ballance (I guess). Even choosing side in this battle based only on your vision, not practical need. Bringing back The Lost wouldn't be your saving hand, if it's your only hope. If you destroy Academy, there's no faith crisis in galaxy. Does anyone, except player, care about winning this quest?

Whose war it is?

From the beggining, we divided on team Science and Religion. Again, choosing team is based on your faith, but does it have any impact on your empire? If you have religious people, wouldn't bringing back The Lost feel like a triumph for them, and making your senate religious for a few turns?  If not, then war is not political, and that bring us to a question of 1'st paragraph. 

I know, I might be late with that Academy theme with next expansion around the corner, but I want this game be better. And that would be ironic, if all problems will be resoved in it.

P.S.: I hope text is readable with my bad english.

the thing alt that quest is that it is a gigantic accelerator, meaning loading the quest makes everyone else a lot stronger.

So the penalty is not so much on you, but the change in relative power