I think that this is a valid question, here is my belief (Gemini):
By the time you have access to paid improvements such as the Academy or Biowell, you likely also have some upgrades to standard improvements. Mines for example have additional energy with Biometallurgy; while farms have additional food, production, science and energy.
Additionally, as the game progresses, there are many opportunities for civilians to fill specialist slots. Unless the tile is incompatible with a standard improvement (snow), I am not tempted to pay maintenance at the expense of an established farm, mine or generator.
That being said, Academies are definitely attractive with 4 Science/1 Culture at full upgrade. If I am seriously lacking in science or going for a Supremacy victory, while rolling in energy, I might reconsider replacing generators/mines with Academies.
In short (Gemeni): I believe that the benefits of paid improvements (Academy) are best achieved through specialists, through large population, through food/farms.