I agree with you! At very first letter of the producer Yoshida said that there would have no character wipe during these changes...but that's exactly what they are doing. The removal of Physical levels is a partial wipe since they are removing something people put effort to raise.

I also agree that, instead of removing it, there are many ways of using these levels so the players won't feel they are removing something we already put effort to gain. I also suggested them a similar idea today, but was a trait system with access similar to FFXIII's crysalis, where you can chose a path and follow it, chosing branchs, to access certain traits this way.