I've been thinking a bit about the reasons why and when I am using real floppy disks. I like my 1541U2 and for sure devices like this are an essential component of modern use of Commodore computers. I have a dedicated desk for my C64. If I take it to the living I usually leave the physical floppy drives upstairs. 1541U2 is often fine for such purposes.
As you might have imagined, I am using a 1571. My good old 1541-II still works fine, but the 1571 is a nice upgrade. There is Jiffydos inside, but my C64 has the original ROM. I can use JiffyDOS on my C64 with the custom kernal feature of the 1541U2, but I often limit myself to the Final Cartridge III fastloader, it is faster than JiffyDOS. So the JiffyDOS in my 1571 is largely unused, except for one crucial feature: Autodetection of single and double sided disks. If you no longer need to switch the drive into double sided mode to read a double sided disk, double sided disks suddenly become much more usefull, and suddenly the 1571 is a real improvement over the 1541.
I often use real floppies in the following situations:
* Software on floppies, I have hundreds of them and regularily use them
* Allthough I agree a lot of software has been fixed for modern storage media, there is also a lot of software that hasn't. Even modern demo's like Comaland assume a 1541, don't run from device 9 and even don't tolerate any other device than device 8 on the bus. While the 1541U2 is 100% compatible, you need to reconfigure it (turn off second drive, turn off IEC device, turn off printer, switch it to device 8), it is much more convenient to use the real floppy drive: Switch on, pull cable from 1541U2, run demo.
* The 1541U2 is a 1541 simulator, so single sided only. Double sided work therefore always on real floppies.
* Demonstration purposes. Many people are too young to have known 5.25 floppies. If you demonstrate your C64 to someone, it works a lot better if you can show a real floppy drive with real floppies. You show what computing really was in the 80's.
Not everything here translates to a Mega65, but I'm convinced that if I will have one, I'm going to connect a real floppy drive. With burst mode supported, even if just for load, it looks like the 1571 is a good match for the Mega65 and without an urgent need for JiffyDOS.