One issue with the "move missions into the world" concept is that a lot of players need a lot of direction. We even had reviewers who would go through the tutorial, get to the world map, and still not realize there were missions out there for them to do, assume the game had no direction, and shelve it.
Needless to say, we didn't try to reach that far down to hold hands (we're not even sure how we could get through in a case like that), but there's also a legitimate reason to have some pretty prominent "you could go here next" pointers.
That said, I agree it shouldn't be flooding the screen with missions; for a long time we had it start with 2 missions per continent and work up to 7. That may have been too few, but our usual practice of doing big changes like a binary-search instead of incremental ones does sometimes lead to situations like this
Well, as a simple suggestion of how to solve that problem, what comes to mind is that the survivors could be attempting to detect opportunities through whichever magical or technological means they have at their disposal, and they could display "missions" on the map that were actually part of a room in that terrain. So maybe you have a room where allied critters are fighting against enemies and you can get something out of helping them, and that pops up on the map with information about it to help direct the player. The mission's appearance would be random, so you'd still find tons of these little things wandering around, but if you were after direction that'd be available.
You could even have an NPC in the settlement (I think a human character would be more fun than an Ilari, though YMMV) who can suggest goals (maybe with a little two-frame talky head!!!) but who you can totally ignore if you want.
The problem from my point of view is the explorable world often feels pretty sterile and samey. You have all these cool game mechanic ideas but they're all locked away in missions. I'd just like to see those game mechanics appear in exploration because that's the part of the game that really interests me.