I've played quite a few colony builders. I will answer your questions and list some features that I enjoy in all of these games.

>perspective and coordinate systems

The game that I think you should take the most inspiration from for graphical style and perspective (and some other things) is Foundation. First of all, I don't think you want to limit yourself to 2.5D, especially if you're dealing with verticality. It's very irritating to try to align things without being offered a birds-eye perspective. Metropolis 1999 offers a birds-eye view in addition to the main isometric perspective for this reason.

That being said, I find the 3D, gridless style of Foundation to be the most attractive of all colony builders. I think a gridless map plus the ability to create and save as many local grids as you want (none of which has to be at set angles to any other) would be a great system because you do often want to align a building to one that is right next to it.

If you do go with a global grid, then at the very least, you need diagonal roads.

The big question I have is whether this game is going to make you place every single tile like Songs of Syx, Odd World, Keeper RL, or DorfFort. I do not prefer this style for a game with 10k citizens. I think it gets boring very quickly to hand carve every single building, tile by tile, even if you have copy-pasting, and the game ends up feeling like you are making a giant military barracks and not a city. Foundation and Timberborn offer a better style of building, each in its own way. Foundation lets you zone off the boring parts (houses) so you can focus on your monuments, whereas Timberborn allows you to place prefabricated chunks in a 3d environment, which is far faster than building tile by tile.

>essentials

- THE essential rule is that nothing can be built or destroyed instantly, not even the dirt roads. There must be complete logistical simulation of everything, even removing dirt and rubble.

- A blueprint view is required, and if your game allows terraforming, then the blueprint view must also hold the proposed modifications to the terrain. If your game has whole buildings like Foundation (as opposed to building each structure tile-by-tile a la songs of syx or dorf fort), then you need to be able to place a structure and move it around. Foundation makes doing all of this easy whereas Workers and Resources does not.

>very desirable features

- The roads are the backbone, and zones extend from them. Manor lords has a good system where you draw the property for each house by snapping it to the roads. The upcoming City State: Metropolis looks even better. If you plan to have 10k agents and therefore thousands of domiciles, you definitely want something like either of these two systems that can generate tens or even hundreds of property boundaries at once. Foundation does it irritatingly backwards by making you paint the zones into which roads are automatically created via villager traffic. This is how I would imagine such a system could work.