I find that Luigi's X100 half-case
really helps handling - the built-in grip makes it considerably nicer to hold, and with the back covered I no longer accidentally press any buttons.
I too was a bit annoyed in the beginning but I've become less so as time has passed - and especially after the case arrived
The only things I ever change while shooting are ISO, exposure compensation and aperture/shutter, so I never have to open the back door.
AF was sometimes irrititating at first but I now know instinctively when to switch to EVF so that very rarely gives me any grief. Of course, it's not anywhere near the Hexar AF in terms of speed and accuracy, but then again what is?