1 ) How 'bout a template system for community-contributed randomized set pieces? Basically like how dungeons are rooms generated using a slightly randomized template in a random series - Break those randomized templates out into external template files. You could still retain control over chest / loot spawning.
Formivore's Walled City Mods uses a good example of a randomized template system, imho.
2 ) More control for server admins. Specifically over tower / dungeon spawn rates.
3 ) Locked doors and keys? Perhaps with keys in dungeon chests, or dropped by boss mobs? Perhaps with even nastier bosses or extra awesome loot chests on the other side? It'd probably be easy to do multiple key / lock color combos as well.
4 ) Use gold nuggets, bars, and blocks for currency. Store them in their own special ui slots, so they don't take up precious inventory space, allowing you to carry a lot. Have mobs occasionally explode into nuggets upon death. Hide nuggets in breakables / chests. Moar lewt!