You know, I wouldn't mind Mastery of Nature being a pre-requisite for the Arcology Project perk, and the arcology decision requiring Mastery of Nature to have been enacted on the planet. It makes perfect sense thematically, and it makes zero sense that Mastery of Nature can be enacted AFTER you already have a city planet. In fact I find this rather gamey since it alloys you to skip making more city districts.
Ecumenopoli are also way, WAY too strong and easily rushable right now. I think this would be a suitable nerf in the right direction that doesn't actually make them worse, which would just make people never use them.
As for Fen Habanis... they really ought to make you require Zero-G Engineering to colonize or "fix" it. After all, you need Mega-Engineering to colonize the ringworld precursors, and why a city planet unhabited for millions of years is in pristine condition is beyond me.
BTW, crappy small tile worlds are what you want for your ecumenopolis. They are so dense that you will hit the building slot limit no matter what, and the bigger the planet is, the longer it will take to build up, and more costly it will be to make all those city districts.