Sorry, I didn't get a chance to read all of your comments before posting so I am sure you covered this, but since the USGBC is weighting these comments I figured the redundancy would be important.

MR PREREQUISITE: STORAGE AND COLLECTION OF RECYCLABLES: I like the addition of batteries, mercury containing lamps, and would petition to eliminate the glass requirement. Glass is dangerous, inert in a land fill, and even in houston were we have the world's largest glass recycler they don't want to pick it up.
MR PREREQUISITE: CONSTRUCTION AND DEMOLITION DEBRIS MANAGEMENT PLANNING: This is needed, and easy to get. Every project can get at least 20%
MR CREDIT: ENVIRONMENTALLY PREFERABLE STRUCTURE AND ENCLOSURE: (Why do you keep changing the names of all of the credits? it seems arbitrary and will just add thousands of conversations over the next two years) These are some of the rarest credits to get already, I like the addition of the additional options that are more in keeping with the goals of these intents. Also, they focus on different scenarios differently which is important. I am concerned about the amount of documentation required for Option 1, it seems to be very different from the others and the most cumbersome to document. It will need a lot of explanation.
MR CREDIT: CONSTRUCTION AND DEMOLITION DEBRIS MANAGEMENT: I like the division into projects with Demolition and projects without. I am not sure that you need a cap for 'heavy materials', recycling is recycling. If you want to reward gypsum recycling, and other more difficult recycling then you could divide the credit in to 75% of heavy debris recycled, and another point for say 35% of 'non' heavy materials that are more difficult to recycle.
MR CREDIT: NON-STRUCTURAL MATERIALS TRANSPARENCY: It is interesting that MEP items are now included. How are you calculating what the 20% is out of, cost, a consistent number of products??
MR CREDIT: ENVIRONMENTALLY PREFERABLE NON-STRUCTURAL PRODUCTS AND MATERIALS – PRESCRIPTIVE ATTRIBUTES: This is good that it excludes structural items because of the cost shift. What CSI divisions? Some MEP items are included so this will be tougher to know what to count and what not to count. Also, what the heck is this? - Core Based Statistical Area as defined by the U.S. Office of Management and Budget statistical area definition updated December 1, 2009. Can't you just specify a distance?
MR CREDIT: RESPONSIBLE SOURCING OF RAW MATERIALS - No comment other than, this is going to be a lot of paper pushing by contractors and vendors. I do like the combination of these points into one credit, but 1 point is not nearly enough for these. Especially considering you are giving one for the next credit. These used to be 5 easy credits to get, now you get one measly point for doing a ton of work.
MR CREDIT: AVOIDANCE OF CHEMICALS OF CONCERN IN BUILDING MATERIALS: Beginning of a red list credit, which we needed. However, because this is such a labor intensive credit in the early stages of this. It would seem that a 20% threshold is high… not that it would be tough to get 20%, but it would be tough to prove this. But it is a start. I have heard it takes 7 hours to track down this information for one material on one job, so you could spend two weeks easy verifying 20%.