I like your idea of regenerating dungeons but I think there needs to be contingencies, otherwise you might end up with a situation where a player will "farm" dungeons, which damages the atmosphere that dungeons are meant to create in the first place. I think that, for instance, dungeons that are near civilized areas should very infrequently replenish, if at all.
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 
