Lots of good guesses here, but I'll add a couple more:
1. Pissed off partners. Some of MS's key hardware partners made it clear in public that they weren't too happy with MS being a competitor. Might be limiting supply as a favor to these guys. Just look at Google's sale of Motorola to Lenovo and the nearly simultaneous Android/Chromebook announcements from Samsung. Suddenly they are getting married and planning to have kids
2. Magnesium case supply issues forcing a need to prioritize versions to be produced. It is fact that MS had supply issues during the early days of the SP1 launch - perhaps they are having trouble producing enough (i.e. more) now?
3. There might be actually be high demand. Unlike the SP1 launch MS aggressively launched the SP2 around the globe - just before Christmas season
4. Already mentioned, but quality problems, especially firmware. Might be holding off a bit until this is fixed
5. Quality problems, take two. I get the impression from this forum and others that MS is aggressively replacing units that have botched firmware - a lot of them it seems. Replacement demand might actually be putting a dent in retail supply
6. Quality problems, take three. MS might have added some aggressive (i.e. time-consuming) production screens in an attempt to weed out problem units before they are boxed
7. Component supply issues. Perhaps they simply can't get enough high capacity SSDs or LCDs - or something
In the end my best guess is that MS is struggling with a combination of smaller issues resulting in a large issue
1. That is what Microsoft did for the first one, it started as limited supply and locations only, but the poor sales (which is normal), lead to bad press, so Microosft opened up and mass produced (too much), and that lead to further bad press
2. Magnesium case is not the problem. I have seen many OEM products with magnesium casing, and never had any problems. All I know, is that I never saw a dyed magnesium cashing, always painted... which suggests that perhaps you can't dye magnesium.. at least not with good/nice results, like you can with aluminum.
Maybe Microsoft will switch to aluminum if they are able to shrink teh battery a bit, and offset the weight increase due to the aluminum.
3. Correct.
4. Perhaps, but all the complaints I read, are NOTHING compared to other OEMs where it's usually packed with people complaining about issues. Surface Pro 2 seams to have a good track record. I think the only big problem is the bent stand.
5. Perhaps. But it would be a mix of refurbished and new.
6. A possibility. But the stand issue should not exists, but it does.
7. Possible. Usually OEMs uses multiple manufactures for every part not specified in the system specs or customized by the user (wirelesses card, and CPU for example). But maybe Microsoft doesn't do that to simplify (as they are new) support, which Microsoft is already having a hard time (device has a few bugs here and there, and they are having trouble fixing hem. It will probably takes 2-3 gen before getting a near perfect experience).
Another thing that was not mentioned is the CPU upgrade. The 4300U was not released at the same time as the 4200U (when the Surface Pro 2 was in development). Microsoft picked the 4200U because it was the closest performing one in term of speed in GHz of the Surface Pro 1. They would not put a 1.3GHz in, is what I am saying. The rest consumed more power, or too pricey.
As every OEM are using the 4200U for their Core i5 model, and possibly larger orders than Microsoft, and done (contract sign) before Microsoft, means priority gets to them. So, Microsoft, switch to the 4300U after seeing that the situation of the 4200U is not getting better. Since the switch I am seeing more delivery of Surface Pro 2's, but it's hard to say.. it could be selling faster than I when I checked as it was the holiday season.