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I have the impression that the Academy was only 50% complete. Here's a POSSIBLE story of its creation:
1. Five factions, as intended, everything is fine.
2. Units were cut, panic ensued, possible solutions were considered.
3. The idea was to create the Academy instead of the Naga.
4. The creation of the Naga faction was put on hold, slowing down the development of the Academy.
5. All of the above + game bugs = a delay in the release date.
6. The creation of the Academy was frozen, and it was removed from the game, along with everything related to it. Only a few remnants remained, such as the faction name and the option to select the faction in the editor.
7. The game was released, followed by hasty patches.
8. The creation of the Academy was resumed, with plans to introduce it into the game as DLC or an addon.
9. The Academy was released in some form.
10. There was a lot of outrage, joy, and everything as usual...
This is just one of the versions I came up with.