I've noticed that the amount of on-chip EEPROM has been reducing, from 1K on the 328P and friends, down to 256B on the 0-series and 512B on the DA (and none on Arm chips). (I limit myself to chips that have an Arduino core available, which is fairly broad).
I tend to use EEPROM extensively for infrequently-changing user data and for me this is a bad thing. Heck, I even used it for temporary bus scan results in one project when I ran out of everything else. I don't really want to add another chip to my designs, even if serial EEPROMs cost pennies.
I assume it reduces the die complexity or frees up space for other stuff, and maybe reduces cost too. I don't recall being asked for my opinion; maybe I missed the email ;)
Yes, I know about the user row, and that flash can be co-opted for the same task, albeit at the cost of additional code complexity/size.
Is it the case that most projects don't use it and its loss is no great shakes ?