It's a design compromise to keep it cheap as well as minimize the lane usage (i.e. no 2x lane configurations).
So it's either 1x or 4x lanes depending on the requirement; inexpensive vs. performance (that can't utilize all of the bandwidth assigned to it for 2x ports). Most of the 4x lane versions however are 4x port, and there's still a performance limit for simultaneous usage and disks that can exceed the band limitations.
They've waited for PCIe 3.0 to "fix" the issue (1GB/s per lane), and even then, 2x ports running simultaneously still get throttled if the disks can actually exceed 500MB/s for sustained throughputs (still 2x ports on 1x lane SATA controllers). Not a big change on the surface, but if a single disk is run, at least they can operate at full band for SATA III (get the additional 40 - 50MB/s out of the disk).