You can easily change in game Academy Size by modifying this file: "$STEAM_ROOT$\steamapps\common\Endless Space\Public\Simulation\EmpireDescriptor.xml" Line 81: SimulationObjectPropertyDescriptor Name="MaxHeroes" Value="3" to something like this: SimulationObjectPropertyDescriptor Name="MaxHeroes" Value="64"
This changes academy capacity for all players, including AI. In save game there is an available hero pool and I'm not sure what happens when it's exhausted, I would not set MaxHeroes value to crazy numbers.
$STEAM_ROOT$ is a folder where you installed your steam ("C:\Program Files (x86)\Steam" or whatever).
----- You could also change line 83:
SimulationObjectPropertyDescriptor Name="TurnsBeforeNewHero" Value="50" Value to something less than 50, but note, AI also gets new heroes every NN turns mentioned here. Would not recommend fiddling with it, anyway it's your game.
In the same file on line 419 you can find hero count increase value of the first technology ("Futuristic Game Theory" which gives +2 academy cap.