Also, as mentioned above, I also hate the lack of an "undo" button: There are too many easily-pressed buttons and organization options lurking about. Swipe too far, and you have to go into the Dates & Lists tab to recover your email.
The biggest hurdle, for me, in replacing the default Mail app with Mail Pilot, is the lack of desktop counterpart. Sure, I could file messages into Mail Pilot's new "MailPilot" folders, but it's not nearly as elegant as its iPhone and iPad counterpart. And I'm not in a position currently where I can use iOS devices as my full-time triage applications.
Though it has a few problems and 1.0 shortcomings, Mail Pilot is certainly promising. It's not quite ready for full-time use yet, but I'm keeping my eye on the app in the meantime.'
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