I don't think you quite realize what kind of microcontrollers would even come with a DDR3 interface. But if you want to waste away a > 500 MHz chip with sampling GPIO and DMAing that to memory (good luck hitting anything close to what an FPGA could do here, that kind of chip tends to come with multiple levels of caching, pinmuxing, ...) you must have a large BoM and power budget.

Point. I think most of the chips I was thinking about are simpler SDRAM controllers.

Nonetheless, I still think that you're grossly underestimating the needs of the FPGA / Logic Analyzer. The product communicates to the PC over USB for instance, performs RAM-level compression and seems to handle some logic-analyzing tasks as well (considering it natively supports I2C, UART, and the like).

EDIT: I think I see where you're coming from now. The next steps then would be licensing issues then. Like whether or not a company could effectively sell the IP-block of the memory-controller and distribute it over the internet (as what has happened in this project).