Nevertheless, I always understood it that the transposition of some pieces into different keys for the WTC may have been a matter of economy, i.e., finding a reasonably appropriate piece and using it rather than devising a new one from scratch. G*d knows he did that often enough in his cantatas, and everywhere else.
I had always understood that too. I don't think it had as much to do with "sounding better" as with "sounding indeed slightly different as different keys should, but isn't my new temperament a marvellous invention in that you can play in all kinds of odd keys without it grating like heck?"
Given, though, the cryptic way in which Bach wrote down his tuning, such that it took 250 years to be noticed, he would hardly have had cause to take umbrage if someone back then had played the pieces in equal temperament or any other they saw fit to use.