A few weeks ago, Mike Hall posted about "Why use MFC on Windows CE?" This was a bit of a surprise to me because you hardly see Microsoft discussing MFC these days. When the Compact Framework was launched, native code got such a bad press that I thought Microsoft was about to kill its C++ developer base. Fortunately I was wrong.
I (re)started developing for mobile devices in MFC and that was a very interesting experience. In those days the best PDA around was a Compaq iPAQ 3870 with Bluetooth and your development environment of chioce was eVC3. MFC seemed to be an obvious choice due to tool support but there were a few shortcomings. The frameworks imposes a document-view model that sometimes you have to fight against. Documentation was scarce (yes, the online help was bad) and your best resource was to read the MFC source files. This was how I got to understand how the framework was designed and why the tap-and-hold always made the dots circle twice. Interestingly you can see this behavior in a lot of the most recent devices on the Settings applets meaning that these are written in MFC (and the double circling bug is still there - sigh).
There is one good reason why you should not use MFC: it is slow. I understood this when I was working on the SqlCeSpy code and found that MFC would refresh a virtual list view noticeably slower than other applications, especially the ones written in ATL. MFC's message handling mechanism is a bit complex and convoluted meaning that when you need to handle a reflected message it gets bounced back and forth before it actually gets to where it is needed. The result for me was a slow refresh of the virtual list view. So slow in fact that it prompted me to write a grid-like control using virtual methods instead of reflected notification messages. Come to think of it, I never published this code...
So what is the best choice? As far as I can tell, when handling a user interface in native code, your best choice is to use WTL, ATL's extension now freely available from sourceforge. The thunk mechanism for handling the message maps make it very fast and efficient to process windows messages and applications tend to be both faster and smaller (compared to the statically linked MFC applications). Also, you feel like having much better control of what is going on and the templated approach is very elegant, although it requires conquering a steeper learning curve. But once you're there, you're hooked.