There are two types of M.2 slots - SATA and PCIe. The SATA type M.2 are exactly the same as a regular SATA or mSATA slot, just a different physical form factor. The PCIe type are what can provide higher speeds that SATA. (Actually, there's a third type which can switch between SATA and PCIe mode depending on what you put into it. But these are fairly rare.)
While PCIe M.2 does provide higher speeds than SATA 3, in real-world use there isn't much difference outside of certain applications. The problem is all the benchmarks measure drive speed in MB/s, while your perception of speed is the inverse (sec/MB, or how long you have to wait for an operation to complete). What this means is the bigger the MB/s is, the smaller the difference in wait time. Imagine you need to read 1 GB of data.
125 MB/s (HDD) = 8 sec
250 MB/s (SATA 2 SSD) = 4 sec (4 sec improvement)
500 MB/s (SATA 3 SSD) = 2 sec (2 sec improvement)
1000 MB/s (early PCIe SSD) = 1 sec (1 sec improvement)
2000 MB/s (modern PCIe SSD) = 0.5 sec (0.5 sec improvement)
See how every time the MB/s doubles, the reduction in wait time is only half that of the previous step? Put another way, if you use the HDD as a baseline:
250 MB/s SATA 2 SSD gives you 53% the wait time reduction of the 2000 MB/s PCIe SSD.
500 MB/s SATA 3 SSD gives you 80% the wait time reduction of the 2000 MB/s PCIe SSD.
1000 MB/s early PCIe SSD gives you 93% the wait time reduction of the 2000 MB/s PCIe SSD.
The other problem is that all the benchmarks concentrate on the fastest speeds - the sequential speeds. But how long you have to wait for the drive is determined by the slowest speed on the drive - the 4k speeds. Even the newest PCIe SSDs are still limited to about 50 MB/s 4k read speeds. Imagine you need to read 1 GB of sequential data and 500 MB of 4k data from a SATA 3 SSD and modern PCIe SSD.
modern PCIe SSD
1 GB / 2000 MB/s sequential = 0.5 sec
500 MB / 50 MB/s 4k = 10 sec
Total time = 10.5 sec
SATA 3 SSD
1 GB / 500 MB/s sequential = 2 sec
500 MB / 50 MB/s 4k = 10 sec
Total time = 12 sec
So even though the PCIe SSD has 4x faster sequential speeds than the SATA 3 SSD, the wait times for the two in this test are within 15%. The slower speed impacts wait time a lot more than the faster speed. It's for this reason I advise people to compare 4k speeds in SSD benchmarks, not the sequential speeds.
Samsung has made some great strides in improving queued 4k speeds (about 1500 MB/s for the 960 EVO). But that's a 32-file queue depth - a depth you'll rarely reach in real-world use (aside from virus scans). And based on a max 50 MB/s 4k read speed, both the SATA and PCIe drives should perform identically at 4k reads up to a queue depth of 10-12.
That's not to say PCIe SSDs are useless. More speed is more speed. Just don't expect it to make as much difference in real-world use as the benchmarks (especially sequential-only benchmarks) might suggest. The few real-world tasks where PCIe SSDs really shine are real-time video editing (loading/scanning large video files), and copying large files (e.g. movies) from one PCIe SSD to another.
So if your motherboard or laptop has a PCIe M.2 slot and the price of a M.2 SSD and SATA SSD are comparable, by all means get the M.2 SSD. But don't fret about it if you have to "settle for" a SATA 3 SSD. Under typical workloads your real-world wait times will likely be within 15%-25% of the PCIe SSD.
and it is less expensive
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