The start of the level should fit it's purpose. For example: Do you want to teach the player, or scare them. If the former then there are no enemies, if the latter then there are.

When the player solves part of a puzzle they should already know where to go next. For example: If you have already tried to open a red door before you found the keycard. Bad example: You throw a switch and nothing apparent happens.

If your map looks like it could be make in earlier tech, that's a failure in it's design.

The start of the level should present interesting choices, or look impressive.

Always change floor height when you change floor textures.

Use special border textures between different wall segments and doorways.

Be strict about texture alignment.

Conscious use of contrast everywhere in a level between light and dark areas, cramped and open areas.

Make sure that if a player can see outside that they are able to somehow get there.

Be strict about designing several secret areas on every level.

Make your levels flow so the player will revisit areas several times so they will better understand the 3D space of the level.

Create easily recognizable landmarks in several places for easier navigation.