I can report that WMV has been deprecated and is not supported in Roku2, with no current plans to do so. The fact of the matter is that virtually no one used it and anyone that was has moved or is moving to H.264.
What benefit is there to reducing functionality? Would keeping WMV support have been detrimental to the operation of the Roku in some way or was the reason truly that you think nobody is using it so it got deleted from the codebase?
The new firmware (4.1.2663) re-enables MKV support. It's still not visible in the official USB Player channel, but the unofficial ones (Roksbox and USB Browser) work. I didn't try WMV yet, but I can do it once I get home tonight.
Note that there still seem to be some problems with the MKV playback, but I want to narrow them down before I post about it.
Update: WMV (encoded using Microsoft VC-1) doesn't work even with version 4.1.2663.