I'll speak for the Linux side, at least for the category of software I'm familiar with (which is RF data collection equipment). Or industrial apps vs. consumer apps.
Windows CE (and its associated tools) IMH fairly recent E) is strongly biased to creating a "Windows Experience" on a small screen. The user input mode emphasizes mouse-like actions. Logons, application selection, etc. all try to be as similar to standard Windows as possible.
If a user is driving a lift truck, or filling a picking cart, or moving material from one place to another, there's a problem.
And it's a moving target - particularly on the .NET side. The Compact .NET runtime is seriously handicapped, and important libraries (like networking, data handling, and UI) are incomplete and versions too often deprecate the previous version. . CE seems to be the stepchild in the Windows family (possibly because there's not a lot of active competition selling to the hardware integrators.)
A nice stable rows-and-columns Linux console is a pretty handy context for many (in my experience most) high-use apps on a dinky screen.
Not much good for games on your cell-phone or Zune, though.
NOTE:
I think ctacke probably speaks accurately for the hardware integrator's side. I'm more aligned with the players further down the pipe - software integrators and users.