dgingeri :
I noticed this when they first came out.
The worst thing is the arrangement of the slots. If all the SATA ports are used, there isn't a way to get more than one M.2 PCIe x4 slot, using PCIe ports 9-12. To get a second, the motherboard manufacturer would have to disable two SATA ports to use PCIe lanes 17-20. In addition, the chipset lanes cannot be used to make a x8 slot at all. This setup severely limits the possibilities on how the I/O can be used. The desktop chips, and the Xeon E3 series with them, are severely limited as to what hardware can be used with them.
You are not considering that M.2 is a relatively new interface and before only one was available. Two is pretty overkill since one is capable of up to 32Gbps connections so what would be the downside to having two less SATA ports?
This is consumer end as well. Most consumers are not going to max out SATA ports and M.2.
The extra lanes were never able to be used to make an x8 slot and the only thing that benefits from that is a GPU, or server grade PCIe SSD but who is going to pay through the nose for that and buy a lower end setup?
If you want more than 2 GPUs you can get the EVGA Z170 board with the PLX chip but again it starts to move into the realm of X99 that is made more for high end enthusiasts who want more connections anyways.