Yeah, but there are ways of dealing with that. One, like you said, is to have dungeons in or very close to heavily populated areas repopulate slower. Another is to scale what a dungeon is repopulated with based on the strength of the nearby/encompassing nations and/or cities. If a dungeon is right smack in the middle of your incredibly powerful empire, it shouldn't ever repopulate with some measly spiders. However, maybe a dragon will swoop down and inhabit it one turn; or some dark, scary monster that doesn't really fear you. When this happens, it shouldn't have the player reaction of "Ooo, time to farm that dungeon again!." It should make you think "Ohh, shit! I can't fight this war with my neighbor and fight off this scary monster!" Basically, it should be made that the phat lootz are not your primary concern; rather, they'd be a reward (or compensation) for forcing you to turn your attention to something you might not have factored into your plans (or for ignoring it and suffering the potential consequences). 

We know that some dungeons will spawn creatures; I think it would be neat if powerful beings occasionally venture out of their lairs and cause some mayhem or otherwise interact with the world. An example Stardock gave us of this is if a wandering NPC adventurer disturbs a monster, but another example could just be a monster coming out to eat

In this post , someone has suggested some ideas about dungeons that complement this idea of repopulating dungeons. I think that is clear that everybody likes exploring the map, and that having the world completely explored is a bit boring, so an intelligent dungeon respawning system is needed.

Returning to scouting abilitties, they can be used not only for seen further and exploring quickier, but also for finding resources. I can be an expert exploring sites or making maps, and have the sight of an eagle, but if i can't distinguish between different kinds of minerals or rocs, for example, I will never be able to find any interesting resource.

So maybe different kind of scouting abilitties  can be introduced (one, for getting info from a dungeon, one for gettinf info from an army, one for detecting resources, and so on...). This allows a deeper unit customization system, and also introduces non-combat skills in the mix, which is something I've always missed in this kind of games

I don't know if this was covered... 

But as a Sovereign and controller of my domain, I should also have the ability to create dungeons as a domain enhancement.  It should grant some type of bonus, obviously, but would also be able to be invaded by my opponents.

One good ability for a spy unit may be better chance to flee from battle.