The index does a pretty good job of picking up all the towns and villages IMO. Though trust me, I can sympathize with the difficulties of making a HUGE map feel well populated, but at the same time not have a crazy amount of objectives.

One thing to consider is, the Assymetric commander will probably grow in strength and numbers as they establish their civ recruitment centers. Obviously, that really depends on how you set it up and how many active players the mission has, but my advice is to not judge the initial Assymetric spawns too closely. Test it over an hour or two and see how they move around. The traditional commander can also fill in the gaps for you while the insurgent commander grows.

Don't underestimate the usefulness of military objectives. I started indexing maps recently and reinforced the idea that "military objects" can spawn just about anywhere, and not ONLY in what one would assume are military places (bases, etc). Some civilian towns will have military objects on most maps, and the military obj module will pick these up (you can see this when debugging the obj modules).

To fill in the gaps, I do tend to make my own custom objectives. I know this can spoil things a bit as the mission maker, but after you place a few, if you're like me, it's easy to forget where you put em. :)

If you want to see a mission on Reshmaan, I have one. I don't pretend it's perfect or anything but I have a good time:

https://forums.bistudio.com/topic/190913-alive-spcoop-1-8-prophet-insurgency/