Edit: If this belongs in the ideas section rather than the forums please let me know and I'll move it over there.
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So almost everything I've seen about the Academy has been requests to allow for it to be disabled outright, or otherwise to nerf it nearly into oblivion.

I feel like this is entirely missing an opportunity to really make the Academy a force in the galaxy, to achieve what was obviously the point of the DLC.

Rather than a straight nerf, I'm arguing that there should be some significant overhauls, which yes, is a significant investment of resources on Amplitude's part for what would necessarily have to be a FreeLC, but a necessary one, especially given how the Nakalim are tooled to lean on the Academy. Right now the Academy is obviously a half faction that doesn't actually behave like any normal empire, instead it claims systems, barely actually uses them as other factions would, and has almost all of the power calculations made internally to the faction itself to counter act the fact that it's a pure AI faction with extra bits tacked on.

So, to start with, Academy Reparations Issues:

• Diplomacy Screen Unlock: You need to meet the academy like you would any other faction. You run into their fleets, you end up getting their contact info, fullstop. None of this 'have to actually find the academy to pay them back' bull.
  
  
• Purchasing Heroes: The biggest issue with the academy reparations, I feel, is that when you tick it off you lose access to all hero purchases. I feel like this is the biggest mistake, and there either needs to be a method of gaining heroes based around your faction specifically, or perhaps even just making it so that you can always purchase your own factional heroes for your empire from the market, or perhaps even those of minor factions if your empire has the most pops of that minor faction out of the entire game.
  
  
• Paying Back Reparations: When the Academy goes on the offense and you are fighting a defensive battle against it (IE: they were in your freaking system), you lose their good will (they'll like you less and less), but won't actually sanction you, at least until they turn full hostile. I would also allow you to pay back by other means, turning over systems to them (more on this later), or sending them ships, other resources, etc. Not just dust (though all items sent to them should pay back less than selling them on the market would, barring planets obviously, given Isyander's goals, he WANTS to hoard dust.)

That would be pretty much the only change I make to having ticked off the Academy's repratations mechanics, which are honestly the most frustrating and unfun mechanics in the game, so let's move onto the Core Academy Mechanics.

• Academy Colonization: Right off the bat, the Academy should never be able to colonize, full stop. Instead have them balanced a bit more like the Hisho in some respects, at least when it comes to the Academy system, but less draconian. I'd have it so that when it's just the Academy itself, it's a powerhouse, but as they spread out their resources and administration across multiple planets, they lose power in the Academy home system itself, but overall increase in it by a minor amount on average.
  
  Instead every faction should be able to donate planetary systems to the Academy, just as the Nakalim can. In return, they get a minor, but importantly PERMANENT buff to relations with the Academy, and 1/4th of the non-strategic resources the system produces (so the Nakalim's whole deal of selling to the academy is more potent for obvious reasons, much as how Vaulter privateering is more potent, while not fundamentally different from what other factions can do), they will also count towards your conquest victory score, and the Academy remembers that you donated them, and your relations are buffed by this.
  
  
• Academy Population Makeup: The Academy's pops should be based around what populations are donated to them when you give them a colony, and importantly, their relationship with you compared to other factions in the game is based in part around the mix of pops they have available. Your core race, and the minor faction racial buffs you have, determine who the pops inside of the Academy 'count towards'. These people remember having been part of your empire and give the academy as a whole a better view of your empire.
  
  
• Academy Fleet Construction: The Academy's fleets should still instabuild, but based around the resources they can afford, and their starting resources are based around the number of players. But only in the academy homesystem. Construction happens normally in all of their other colonies, and they can only construct 1 full fleet a turn at the Academy this way. It can have any composition and be instantaneous, which still gives them an overwhelming advantage in a war of attrition, but it keeps them from just starting the game with a dozen or so doom stacks.
  
  
• Elections and Donating to the Academy: The Academy can be donated too at any time, not just when it asks for things, but it still has rotations on the various jobs, it's just a running thing with a count down and 'official running' period when the academy asks for a specific kind of donation and that specific donation counts for more than it normally would, whether it be ships, planets, strategic or luxury resources, or dust.
  
  The elections should be based around your reputation with the academy. If you're friendly with them, your stuff should count slightly more provided it is the requested resource. (Your rep won't effect other resources donated during the election cycle, just boost the requested one harder).
  
  
• Reputation with the Academy: The Academy MUST remember who has been in it's good graces, not just reset every freaking time. As stated above, it should be a combination of permanent buffs (how many systems have you donated to them), relative buffs (what is the racial make up of the academy's colonies), and decaying buffs (how much have you donated, and since when, and when was the last time you held an academy position).
  
  

• Role Related FIDSI Buff: Firstly, each of the roles has one of the FIDSI scores tied to it, and you get a portion of the academy's FIDSI score added to your empire wide one based on which role you take on. I would suggest Science for Librarian, Influence for Vault Keeper, Dust for Master of Dust (obviously), and either Food or Industry for Spear (or perhaps a very small trickle of the strategic resources available to the Academy instead?)
  
  
• Role Quests: Each of these roles must come with some responsibilities, and these responsibilities should be primarily targeted at whoever is the front runner, or the last placer, in each category, and assigned at the beginning of the tenure.
  
  For example, the Spear of Isyander might be told he must defeat X number of ships in battle, including his own (which will inflict heavy empire happiness penalties on his empire if he turns the academy fleet onto his own fleets, this would discourage the players who are already built up in military power from trying to get this massive advantage), he might have orders to conquer systems for the Academy from a certain faction, meaning that his conquests boost the academy, not himself (he would not get the resources from these worlds as he would have if he donated them, and conquering and donating them doesn't meet the reqs of the quest given with the role), or he might be told he needs to weight in on the side of a losing faction and tip the balance towards them, which would result in his empire being embroiled in a war he had no part in, and would be stuck with even if he later lost the position if he didn't finish it off with the fleets.
  
  The idea is that the Spear of Iysander position is powerful as all get out, but you're expected to wield that power for the Academy, even at the cost of your own empire. The goal then is to try to complete the objectives given, but also find ways to benefit yourself in the process. Similar 'quests' would be given to each of the academy positions. The Librarian might be asked to go out of his way to study a specific number of techs, which the Academy would gain too, or to promote the science of other factions by some means. I got nothing for the Vault Keeper, but the Master of Dust would obviously be something something 'help this other group boost their economy' or 'surpass the economy of X faction' etc. The idea being that the quests should exist to promote infighting in the other empires, to drag down front runners, or to boost the people in the back ranks, and give the position holders the capabilities to do so even if they normally wouldn't have them. (And we already know that there is a structure in place for this with the whole Academy/Iysander end questline where you can totally go after people who are otherwise your allies based on their decisions).
  
  Finally, there has to be a cost to failing these quests. Obviously a huge hit to reputation with the Academy, but also, a debuff for your contributions during the next election cycle, so that they count for significantly less, across the board, as the Academy isn't really interested in you retaining the position or getting a new one. This will go away after the next election cycle.
  
  
• Altered Librarian Mechanics: Maybe the Librarian should be able to purchase techs the academy already knows, as well as information, perhaps it should also be able to request the locations of unique planets, the best uncolonized systems, etc. Maybe even 'lock' information away about certain systems, forbidding anyone without an actual unit in the place from seeing into them or recording information about them.
  
  
• Altered Vault Keeper Mechanics: Vault Keeper I think should be able to gain access to the 'leading faction' buff of the political faction whose laws they take on, and maybe get some actions to sway the political factions of other empires, things to change the political leanings of populations both in their empire and others, not much impact on dictatorships except by making rebellion more likely, but a serious impact on every other type.
  
  
• Altered Master of Dust Mechanics: I got nothin' for Master of Dust. Maybe some kind of access to Academy 'trade networks' or something?

Saving a Second Post for Storage of Ideas, either my own not directly relating to balance, or suggestions from others to pour into this pile

Further Balance Change Suggestions

Altered Master of Dust Mechanics and Quests

• Arkdelta's suggestion: All Academy Systems count as Subsidiaries for the Empire that qualifies for this position, has to keep the trade lanes open.
  

Arkdelta wrote:

Possibly your Altered Master of Dust role could involve gaining access to the systems owned by the Academy as Subsidiaries (as if you hade a trade pact with them and they had subsidiaries buit on all their systems) alongside the responsibility of maintaining the security of those trade routes.

New Additions/Radical Change Propositions

• New Academy Role: Linked to Food, based around population/racial/minor faction manipulation.

Your idea is sound, I support that opinion. If the Academy exist as a Separate Faction, they should act like one, but not like just putting their AI Setting on the default militaristic conqueror one that they have in the DLC. A Strict Isolationist Type AI setting would be more preferable and a good start. I just hope that Amplitude would take this matter personally and do the overhaul on this part to making it more.....real and has common sense, like a papal state (which, by definition of the academy, it's technically is one) that initially limited itself with only one system/state, but not averse to donations like you state.

Also regarding the diplomacy, by the act of meeting any part of the Academy should be enough to fulfill the "Finding the Academy" Quest line and subsequently, revealed the whole Academy's Systems too.

Having the Vault Keeper Title will be in charge of taking care of Production and System Improvement other than Science and Dust. (That's for Librarian and Master of Dust's Role, Respectively), and their quest could be regarding Wellbeing, like increasing food, industry production, or keeping certain System Happy, Passing the Requested Law or ensure requested Political Party a seat in your Empire's Senate in the Next Election.

Of Course, All Roles will have provided a Science Cost Discount in Each Respective Research Path, Admiral for Military, Librarian for Science, Vault Master for Empire, and Master of Dust for Economic, but not too much to the point of being unbalanced, just a slight advantage over others.