This is happening to me too,
I have a generic (case is unbranded but drive manufacturer is Sony), external USB FDD and it appears on System Information under Hardware > USB > USB 3.0 Bus, but even when I plug it in with a diskette inserted the drive does not appear on the desktop.

However, with this MacBook I'm able to plug my FDD on my Windows 10 Boot Camp partition and it works perfectly. I don't think it has anything to do with the port being USB 3.0.
It also works on my iMac running Yosemite. I think Apple could have dropped support for FDD's on the latest release of the OS.
I'm currently upgrading my iMac to El Capitan so I can try to confirm if this issue comes from the OS.
If anyone finds a solution please advise.
Regards,