It's the poor adaptability.
The Canon FD (and earlier) bodies had the shortest film-flange distance of popular SLRs. When the EOS line came out, Canon made them slightly deeper and thereby eliminated the capacity for FD lenses to be mounted on EOS bodies. But as has been said, the EOS is an all-electronic mount while the FD is all-manual. So at the time it was not a big deal - people wanted the AF badly enough. And the late 80's EOS bodies had the kind of user interface that many now consider "dSLR" standard - they were revolutionary at the time. I mean, being able to adjust shutter and aperture without moving your finger off the release!
As has been said, the release of mirrorless bodies means that all manual-focus SLR lenses are fair game, and all-mechanical mounts are easier to adapt (because the aperture stop-down can be incorporated into the adapter)
I personally think we are coming to the end of the "boom" in used manual lens prices across the board. Old lenses were a fashion. Some photogs will persist but IMHO the FF mirrorless cameras won't affect FD prices that much. The reason is that the A7 twins cost a fair bit of money, and are pretty high resolution. Buyers will be putting glass they are familiar with, and know to be high quality, in front of them. For that reason, the long-dead FD line will be neither new enough to be "the greatest lens in the focal length" nor old enough to be truly "classic."
I think backwards compatibility isn't sought-after that much in reality. If it were, Pentax would have eaten Nikon and particularly Canon for breakfast. Every K-mount and even (standard) m42-mount lens can be used on a Pentax dSLR. The only limit is that the m42 lenses have to be manually stopped down (but they all have a switch for this anyway.)
Anyhoo, if you have something to attach them to, the FD lenses are good value. Minolta manual focus lenses also have no direct compatibility with modern SLRs and are also good value.