Maybe it's just me, but it sounds kind of bad to hear the director say he couldn't figure out how to make his own movie work.
Honestly, there's nothing worrisome there. That's just par for the course. Very few movies (or books) are perfect from conception; part of the process is trying something out, deciding it's not quite working, and working with your collaborators to find a solution. Script doctors and reshoots and all that are not necessarily ill omens; it simply means that your work-in-progress is just that.
(I'm currently slaving away on the third draft of a book, and I'm fully aware of what parts are fine and which still need work. And so is my editor!)