Environment design for levels/missions seems to be a very tricky thing to get right.
My favorite resource on the topic is from Bungie:
Environment Design in HALO 3 by Mike Zak. It goes through some great detail on how they design and built up their levels, and dealt with AI.
Here's the halo 3 whiteboard for the factory level:
Alex Galuzin has some nice introductory material on Level Design Work Flow and Planning levels. Also check World of Level Design.
Basics of good design are also covered in Brian Upton's GDC 2007 talk on Narrative Landscapes.
There are some good tips on environmental storytelling by Don Carson, part 1
Ben Cousins gives some good metrics to evaluate a map in Low-Level Game Design, Atoms, Measurement and Hierarchies, and Cevat Yerli illustrates some great examples of how a map can be effecitvly laid out in "Crysis in the Making".
Finally Realistic Level Design in Max Payne by Aki Määttä covers some details on indoor levels.
Alright, you should be all up and ready to make some awesome levels now!