I almost wonder if terraforming should be reworked. Like instead of opening up usable squares on the map, it either changes the planet globally or allows you to utilize hostile planets.
I do like the idea of zoning planets based on terrain and specialization (eg, you have a part of a continent that is grassland, it becomes a farming district, etc), but I'm not sure it works when lined up with a geographical map, adjacency bonuses, and buildings. One side of me finds all that very appealing, but another side finds it very frustrating too. A side of me prefers having buildings all just being in the capital, but they do work nicely with adjacency bonuses. I guess what I'd probably like would be a cross of MOO2/GC1 and the zoning of GC2/3 and MOO3.
I'd almost prefer zones to be more abstracted where its not directly tied to the geography of a planet map, but tied to the planet size/habitability instead (eg, a small arid planet you'd get 2 rocky zones, a medium terran you'd get 3 fertile, 1 rocky, etc). Maybe terraforming can be used to change the type/quality of those zones.
I think a more simplified form of zoning would work nice for non-major (resource generating) planets. Just zone it, forget it, and move on to the next planet.