It is just incredibly stupid to program flash memory with a very low-level interface designed for controlling spinning disks. You could extend ATA enough to give a raw flash (erase this block, then write with this data) or semi-raw (distribute write this block to nand chips 1,3,5,7, ...), but it still doesn't change the fact that the bus and protocol are engineered around spinning disks and overcoming its latency problems.
Other problems with sata (and pci) is that they are incredibly power-hungry busses.
While we have some interesting NAND flash-optimized code in linux kernel (UBIFS), microsofts dominant position in desktop market means they only appear in embedded systems. Instead of using flash-optimized free software filesystems, we attach a cpu on the flash chips to emulate the behaviour of a hard drive - just to keep microsoft operating systmems happy.
How much more evidence do people need that microsofts monopoly stiffles innovation?