In fact, equal temperament as a concept was known and discussed by theoreticians since at least the 16th century, and was advocated as an ideal solution for tuning and adjusting frets on fretted instruments (namely the lute and the viola da gamba). But equal temperament stayed more or less a theoretical concept, though players of fretted instruments apparently employed an approximation of equal temperament.
Actually, it is important to note that the problem of temperament is generally related to keyboard instruments, which have a fixed intonation, and 12 notes to the octave. Not so on wind or string instruments.
> I like natural intervals, but dividing the octave in 12 tones is a rather inappropriate way of using them.
This is a gross misunderstanding of how we came to have 12 notes to the octave. Actually, depending on how far back you wanna go, we started with 6 notes (the hexachordal system), ut (C) to la (A), to which were added the mi and the fa of the hard and the soft hexachords, which became B and B flat. The rest of the black keys on the keyboard came from further modulating the hexachords.
In the 16th century, there were actually numerous keyboard instruments built with more than 12 notes to the octave, reaching 19 notes and sometimes even 31 notes to the octave. Having separate keys for e flat and d sharp meant being able keep using meantone tuning while playing in such remote keys as b major and d flat major.
> It's not the ultimate system nor the end of temperaments, but it's been really, really useful.
That's true, it's a practical system which makes instruments more approachable and makes it easy to play together, but there are downsides: ET removes a lot of the charm of harmony (all keys sound the same and all chords are more or less discordant). Equal-tempered thirds are actually very discordant (that is, out of tune), but people have become so used to ET, that you play them something in meantone and they'll claim the pure thirds are out of tune!
> To me, it's pretty clear that the WTC is Bach gleefully exploring the freedom of transposition-invariance and free modulation. In other words: Bach would have loved the equal temperament, and this article would likely give him a hearty chuckle.
While Bach was known to have been critical of mean-tone tuning, he was, according to evidence, a practical guy who employed the practices of his time.
Yes, one can imagine that he would have preferred equal temperament to well-temperament. One can also argue, and many do, that Bach would have preferred the piano to the harpsichord. Maybe he would have also preferred a Yamaha D7 to a pipe organ. One can imagine...