I thought a lot about terraforming and still like to have EP (Environment Points) for that
Maybe the system could invited without much micromanagement: Every planet produce EP per Turn depending on the environment e.g. Gaia -> 10, Good -> 6, Adequate -> 2, Poor and Hostile -> 0.
Set the focus on EP may give 0.5 * Pop in EP per turn, so you can rush some terraforming projects.
Organic Growth specials could provide +3 EP in addition to their pop-bonus (would make it more interessting to have them more than once)
EP could be spent for:
1.) terraforming (+max Pop, replacing Pop techs - have to be researched)
2.) atmospheric terraforming (changing the environment - like terraforming now)
3.) Pop-Growth on one specific planet (rush pop-growth - like housing in MOO2)
There are different possibilities to implement a system to spent EP:
1.) You need a ship with a "terraforming module", that could perform terraforming and atmospheric terraforming. The module is not consumed by terraforming, but the project costs EP. There could be buttons for "terraform +3 pop", "atmospheric terraform clockwise", "atmospheric terraform counter clockwise". That would enable you to terraform an unoccupied planet. Pop growth project could be something like a policy but cost EP (either once or the whole time it's active)
2.) EP are managed like policies: If you have enough EP you choose a planet and than a project.
3.) EP are managed like production with a list. (I don't like that but want to mention it nevertheless)
I know, it would add an additional ressource beside pop and influence, but I think with the proposed system it is easy to handle. Especially the way 1.) would make the tall an option because you could terraform planets before settle them. On the other side you need at least one ship and sufficient EP to terraform, which prevents it from being a no brainer.
I think Gaia should still be a production project because it's mostly a huge computer to build.
Even if all your planets are good or even Gaia, there is use of EP to let your colonies grow. So I think even in endgame it's an interessting mechanic.