> another problem it's created is that flash has a limited number of write cycles

SPI flash typically have somewhere between 10k to 100k write cycles. Without wear leveling, lets say a write is made on every boot, and lets say a machine is booted 3 times a day you are still going to have a 9+ year life on a flash chip with only 10k writes.

EDIT: Did a search for a random "replacement SPI flash MSI" and found an MX25L25673G being used. Using that as an example it has 100k write cycles, using 3 writes a day, that's like 91 years. Basically flash memory is at the point where its "good enough" not to worry about.