I've heard a patch is coming so a few notes from me:

There is a bunch of issues, which are noticeable especially while playing Umbral Choir:
- Academy systems cannot have Sleepers installed (what quite simply makes little sense, they are no different from regular faction systems),
- Academy systems cannot have Sanctuaries. This one is actually important because if an Academy colonization ship keeps orbiting the same system without colonising it then the system holds a Sanctuary, what ruins one of the UC's main advantages: stealth.
- It's probably to compensate for the shortcuts but the fact backdoors on Academy systems are free can on the other hand be heavily abused in some situations, again, especially if one plays as UC.

My recommendation would be to remove the free backdoors and make it possible to install Sleepers/Sanctuaries on Academy systems instead.

Some more problems with the Awakening are:
- Presence of Nakalim in the game hits the Sophon tech cost bonus a bit. Becomes less noticeable the more major factions are in the game, hits Sophons hard in 2-3p though (and Sophons are not the most powerful faction already).
- Power of the Academy fleet should scale with game progress so the fleet is less overpowered at the beginning and less useless in late game. This is especially problematic in terms of invasions (Academy fleet allows to invade at the stage so early when there's no real counter to that available; the AIs seem to be aware of it and always pick Spear of Isyander as their role prioritiy).

Not really bugs but suggestions:
- Master of Dust is almost useless. Maybe if Academy dust could be spent on buyouts it would be worth some consideration.
- Librarian is also useless. If it enabled minor faction laws it would however become a tempting choice.