The M.2 form factor isn't that conducive to having lots of them, since they're on the board and need large connectors and physical standoffs. They're also a pain in the ass to install because they lie flat, close to the board, so you're likely to have to remove a bunch of shit to get to them. This is why I've never cared about and mostly hated every "tool-less" M.2 latching mechanism cooked up by the motherboard manufacturers: I already have a screwdriver because I needed to remove my GPU and my ethernet card and the stupid motherboard "armor" to even get at the damn slots.

SATA was a cabling nightmare, sure, but cables let you relocate bulk somewhere else in the case, so you can bunch all the connectors up on the board.

Frankly, given that most advertised M.2 speeds are not sustained or even hit most of the time, I could deal with some slower speeds due to cable length if it meant I could mount my SSDs anywhere but underneath my triple slot GPU.