You can't do individual branching for every single strand of computation for a typical GPU. With their chips they are trying to create a "third" category between highly parallel, but few individual instruction threads, and normal CPU's.

And the $99 is not for a mass produced card or chip, but for an initial small production run computer that includes one of the parallela chip.

You pay for a dual-core ARM computer based on the Zynq SoC (which means you get an FPGA in the deal) with an Epiphany chip. Getting a Zynq dev-board for that price in itself makes it worth it for a lot of people.