I've been mulling this over for a while, and decided to implement it in the next week or so. The reasons: publishing two HD versions of a movie is using up phenomenal amounts of disc space on the server, and I'd like to delay filling it for as long as possible. More than this though, as you know, I use Macs and edit content in Final Cut Pro. The native output is Quicktime. By encapsulating this in an MP4 format, a lot of the quality of the original is maintained. MP4 is now the most widely used format for videos, and can easily be converted to run on any mobile device, such as iPads and iPhones. WMV, on the other hand, is the result of passing the Quicktime file through a conversion program. No matter how good the software, and I've tried quite a few conversion programs, none of them do a really good job. This means that the resulting WMV file, and any derivatives you create from it, will never be great quality. Given that MP4 plays on all platforms, it seems the obvious choice.
One thing I will do when publishing MP4 only; I will increase the bitrate from 5 Mbps to 6 Mbps, making the file about 15% bigger. I still benefit from a lot of saved disc space, and you get a product which is even sharper than before.
Please leave feedback if this decision matters to you.