The one thing where I think the Floppy Emu has an advantage is in games that require a lot of disk flipping. I was trying to play Competition Karate the other night (one of my favorites from my youth) and it was *torture* on the CFFA3000. Maybe there's some shortcut that I don't know about, but it seems like the only way to "flip" a disk in the CFFA3000 is to cmd-shift-esc, select the CFFA3000, select "assign disk II volumes", select side 2 of the disk, select drive 1, then esc, select quit without rebooting, and select quit from the control panel menu to get back to the game. That's a pain in the ass to do even once, and Competition Karate and some other games like it require you to do it over and over.
This was annoying but not such a hassle with an actual physical disk. It was a lot quicker.
Some games also don't let you get into the control panel menu to select the CFFA3000 to eject the disk. I'm not sure what to do in those situations.
With the Floppy Emu, I think this same thing is accomplished with 2 or maybe 3 button presses. It's been a while since I used mine, but I'm pretty sure you just press a button to eject the first side image, then select the second side image from the list (which should be just below it, unless you have some crazy naming scheme). In this case, it's an advantage to have an external device with its own screen and controls.
Again, please do tell me if there's some shortcut way of doing this on the CFFA3000, because I've decided I just can't play games like Competition Karate with this card otherwise. It's too painful.
In other situations, though, you're right that the CFFA3000 is a better experience than the Floppy Emu. I still think the Floppy Emu is a great device, though.
This is what the CFFA3000 remote switch is intended for. If you add each disk to the Disk ][ assignment screen, you can cycle to the next disk by pressing the respective button on the remote. So advancing to the next disk (in a set of disks) usually requires only one push of a button.