The enemies are set on a respawn timer. So eventually all those cleared dungeons will be teeming with all sorts of baddies again.
There are some mods on SkyrimNexus that change the Respawn Times of creeps. You can add the files to your game for specific spawn times, one a day, every 2 days, once a week, etc.
Also there is a Real Time mod, changes the time to sync with real world time, instead of 1 game hour = 20 RL minutes, 1 game hour = 1 RL hour.
For those of you that also want to up the difficulty of your game considerably there are two mods you should check.
The first is a mod to Slow Your Leveling and the second is a mod to make Everything Harder - Fuzzys Realism Mod: No quest tracking, no map, no compass, etc.
These might make your game more interesting and difficult for those who thinks its too easy.