I've been following the tuning debate with interest, and I've spent a happy few minutes listening to some of the excellent samples on Brad Lehman's website.
Just a couple of thoughts. Part of our fascination with Bach is that he successfully pursued two simultaneous goals -- musical and theoretical perfection. The 48 preludes are fugues are wonderful music, and also a masterful demonstration of technical skill, and I find the idea that Bach provided the clue to an appropriate tuning system on the title page perfectly plausible.
However, perhaps this tuning system was just the last piece in his *theoretical* jigsaw puzzle. A previous set of pieces, the 2 and 3 part inventions, also involved a clear key scheme: a rising scale, with major and minor pieces on the white notes from C to A, a minor piece on the white note B, and major pieces on the black notes Bb and Eb. This can be seen as summing up "normal" practice, pushing the unequal tuning system to its expressive boundaries (as far as F minor, for example), and enjoying the enharmonic surprises when they occur.
The "48" approach is completely different, presenting a piece in C sharp major not for its particular expressive qualities, but just as a piece. Perhaps this was Bach (not for the first time) looking "forward", compared to "backward" (or maybe sideways) for the inventions.
I could also raise a heretical point here. We are so used to the unfairness of the universe in depriving us of perfect thirds and fifths in all the keys that we ignore something that actually works in our favour: the more sharps or flats there are in the key signature, the easier it is to transpose a piece into a familiar key. A piece in C sharp major can be read quite easily in C major, for instance.
So, to sum up -- perhaps the temperament indicated is proposed as a satisfactory *theoretical* solution to playing the pieces as written, but at the same time as a departure from normal practice. Would practical musicians not simply have shifted the more difficult pieces into more accessible keys? Was Bach just in a theoretical mood that day?
Benjamin Waterhouse