I find that I don't miss more shots with the X cameras vs. an M. Just different shots. My hit ratio is better with the X cameras than it ever was with the M. I sort of wish this was not the case but if I'm critical about it, it's true.
I generally agree. The X-Pro1 is an autofocus camera, and works best when autofocusing. No matter how fast your autofocus is, however - and the X-Pro1's autofocus is not fast - it's never going to be as fast as manual zone focusing. Of course, that can be done with the X-Pro1, too, but the lack of a DoF scale on most of the (excellent) Fuji lenses makes this cumbersome.
The answer is manual focus lenses with DoF scales (with the caveat that the scales are 1.5x too conservative due to the crop). But if I use those manual focus lenses on the X-Pro1 and I DO want to focus precisely, it becomes difficult because of the lack of a focusing aid.
With focus peaking, I get everything I want out of the X-Pro1: an autofocus camera with excellent glass AND a capable manual focus camera, too.
To be clear: when I'm shooting things that allow me the time to autofocus, the X-Pro1 keeper rate is very high. It's just, as you say, that the images are different to those I take with my M, and, as you say, I wish that were not the case.