In special rooms with zoo-like generation, meaning they generate a monster on every square, generate the monsters with MM_NOGRP to suppress group generation. This prevents a group from being one of the last things to spawn into the room and overflow into nearby spaces outside of it.

Monster lairs (antholes, cockatrice nests, etc) are not filled wall-to-wall with monsters.

Certain special rooms (typically ones that have awake monsters in them that shouldn’t wander around the level) always generate with all of their doors locked.

Add a “specialness” value to each special room and possibly dungeon feature, based on their approximate usefulness to the player. (For example, a swamp room is virtually useless to the player, a treasure zoo not very useful, a throne room more useful, and a temple or shop the most useful.) A level will start out with some amount of specialness available, and randomly chooses special rooms and features to add until it runs out of specialness.