The early history of the pipe organ in France has some gaps. In the mid-16th Century, stop lists and scattered notations about registrations in France do not seem to be notably different from those found in Italy or Northern Europe. But the first writings of the "French classical organ school" (Nivers, 1665) already contain a very different set of specifications that would remain almost unchanged until after the Revolution of 1789.
The most obvious peculiarity of the changed esthetic is the emphasis on reed stops and imitations of reed sounds achieved by combination of mutation ranks. Dutch organs could have produced similar sounds, certainly, but it is only in France that we find whole suites devoted to the exploitation of krummhorn, cornet, trumpet, and "grand jeu" sonorities, often without a single intervention of the traditional plenum. At the same time, the cornet (perhaps with an additional trumpet) got a manual of its own, facilitating conversations among these sonorities without the need to change stops in a middle of a piece. (The cornet, a combination of five flue ranks, was nevertheless considered a reed stop by some organists.)
In the rest of Europe, when a piece from the Baroque era requires a big finish, historical data suggest we should use principals plus mixtures and cymbale (i.e., the plenum, all of the these ranks being flue pipes of "normal" scale), perhaps with a posaune pedal. But the French composers headed straight for the "grand jeu", a combination of reeds, cornet, and additional components reinforcing these timbres. The plenum ("plein jeu") appears only rarely, usually in isolated movements of special liturgical significance such as the first verset of the Kyrie or the Sanctus. Was this emphasis on reed timbre just a fad that lasted 150 years? Perhaps a fascination with the nasal sounds of many pastoral instruments of the French countryside? Or were the pieces that were actually written down and published designed to provide examples of unusual coloristic movements that most organists were unable to improvise? (In this last scenario, the "normal" sound of the organ plenum would have been used for most "ordinary" music, either improvised or else so well known that they never bothered to write it down, thus explaining the apparently lopsided repertoire.) These are speculations; I do not feel the esthetic of the period has been satisfactorily explained.
Perhaps the most paradoxical feature of the period is that the French, while uniformly praising spontaneity and the superiority of (their own?) good taste over rote learning, still found it necessary to provide detailed recipes for their registrations, even though the same or very similar recipes had been published many times before, and even though most of the instruments were configured almost exactly alike. We get the impression that the illusion of infinite musical variety and contrasts was supposed to be created through the adroit use of a fairly short list of tone colors.
The tonal esthetic of the French classical organ, in fact, requires the appreciation of the pure essence of the flute, the cornet, the krummhorn, the trumpet, the "plein jeu", and the "grand jeu". It is completely antithetical to the 19th Century idea of subtle gradations of timbre and volume. Such variations of registration as the composers suggested seem intended mostly to achieve a better balance, and usually not to produce new timbres.
There were, of course, tinkerers. Mersenne reported an inventor who had devised pipes capable of producing each of the vowels—and I am sure he thought, "Now if we can only produce the consonants, we will really have something." But these novelties never caught on, not for lack of ingenuity, but because the beloved cast of traditional characters in the organ loft already worked so well together.