Trees tend to hide the machinery during the stage 3, so you end up playing "find the pixel" when you're at 99% deconstruction. It would be nice if say hovering over the deconstruction panel highlighted all the machinery you still have to pack up.
I would say stage 2 is the best part of the game. The interplay between the biomes, how they both compete and help each other, and trying to figure out how to fit enough of all them, is fun.
Stage 1 is fine, although a bit repetitive from one session to the next. Excavator to new area, calcifier, wind turbine, detoxifiers, greenhouses, repeat. Adding another way to extend greenery that breaks this cycle (while contributing or benefiting from it) would help a lot.
Stage 3 feels very disjointed. It's very cute conceptually, but the steam turbines, deconstruction pilons and drones are like 3 different mini-stages each, with little connection between each other, and not enough meat in any of them by themselves to be actually interesting. It also suffers in that, unlike Stage 2 that still makes use of Stage 1 buildings, it is very self contained. You hardly have any reason to make use of any Stage 1 or stage 2 buildings by then. Which makes sense thematically, but doesn't help with the fun factor.