M.2 and SATA are not comparable technologies.
M.2 is a port design that can leverage both SATA 3 and NVMe storage.
I guess you meant SATA 3 or NVMe. M.2 would be good to use anyhow as it saves a lot of space compared to 2.5" SSD's.
SATA SSD's are quite cost-effective, NMVe is quite a bit faster, but for now, much more expensive.
I think it's possible to implement M.2 with AHCI backwards compatibility so one can mount both SATA 3 and NVMe M.2 SSD's.