I have seen the complaints about the Academy faction and agree with many of the sentiments.  In particular, I don't like the following aspects of the Academy:

• The Academy can claim systems at a rapid rate and get in your way when trying to expand your empire - particularly if you are unlucky enough to spawn near the Academy.
• The Spear of Isyander is overpowered.

After playing Endless Legend with the Symbiosis DLC enabled, I have noticed similarities between the Academy and the Urkans in Endless Legend. Both can (at least temporarily) claim systems/regions, and both can provide a high-powered unit as a reward. However, Endless Legend makes the Urkans less of a problem in a very simple way: you can simply uncheck the Urkans box in the Game Settings which disables them while still leaving the Mykara faction enabled. If I don't feel like dealing with the Urkans, I uncheck the box and then I don't have to worry about getting raided by lice, being unable to claim a region, getting destroyed by another empire using tamed Urkans, etc. It would be nice if similar set of Academy options was added to Endless Space 2. However, in the case of the Academy, I could see two switches/checkboxes being useful in the Endless Space 2 Gameplay Options:

• Disable Academy colonization
• Disable Academy roles

I realize that there is a larger discussion to be had on how to better balance the Academy as a whole, but I haven't played as the Nakalim much yet so I don't have any good suggestions at the moment. However, these additional options would provide a quick fix for now because those who don't like a certain aspect of the Academy could simply disable what they don't like, and those who feel that the Academy is fine the way it is can continue to play with the options enabled.

Yes please, just a couple of sliders would solve the issue of games not playing out the way we want! 

Options like:

-> Academy Grant Start. Options to delay the first Academy voting event 0, 20, 40 turns.

-> Academy Expansion Speed. With more than two options. On the slowest setting it should not expand more than once per 15 turns.

Also, possibly add proper scaling to Spear of Isyander manpower capacity (First grant period only is the issue). But even if the above 2nd point is implemented I'd be fine without it changed.

I really think these will reverse the community's opinion on this otherwise brilliant expansion.

Been having a lot of fun with it lately tbh, getting Spear and running over my nearest neighbor at the start of the game ftw so not really complaining. Game is still hard. Great expansion!

I guess its really a non-issue. The realization that the Academy grants can only begin once the Academy is found adds enough randomness to the equation to satisfy me.  I'd rather the focus was on fixing the very minor bugs and inconsistencies in the dlc. Its also sad that the flagships from the grants pretty much never get used, since they require such a large dust investment in the early game.