2 + 2 <> 4. Whatever he did at Cincy isn't working at ND and that likely is becuase ND plays a much harder and diverse schedule. Cincy played in a weak conference and against the same teams and systems every single year. ND plays unique teams per year and overall plays a much harder schedule, thus things that won games 42-38 at Cincy lose games at ND.
People thought he could train new QBs quickly and at will. The "flip flopping" you see now is people realizing that was a false assumption. People are now throwing darts at the wall at what exactly the QB needs to be that can run his system -- with the most common hypothesis being at ND against the type of schedule we play it needs to be a QB that doesn't exist or is a once in a lifetime QB. Thus, the more logical path is to change the system to what a larger pool of QBs can master within one year.