Here's a few ideas I thought I'd share, I apologize if any of them have already been suggested:
1) CMOS temperature displayed constantly above or below ML menus. I like to keep an eye on the temp.
2) Easier to use/understand rack/stack focus. There's got to be an easier way to implement this feature, a lot of people have trouble figuring it out.
3) It would be nice if we could use a remote shutter switch (e.g. RS60-E3) to trigger the rack/stack focus feature instead of the [SET] button. This would obviously be great to prevent camera shake while recording.
4) Holding down a button to have it advance quicker through the settings rather than having to press it repeatedly (mostly for things like the zebra range and other large value ranges).
5) Finer tuning of CBRe (instead of jumping from 50 to 60 allow selecting 51-59 too).