For something this powerful, you might make it into a while-house automation controller or large CNC machine, and you probably wouldn't want to hook up the IO directly to the main CPU... You'd use Ethernet for distributed IO, maybe I2C for local IO (combined with something like this: https://www.adafruit.com/product/732, which would provide much more powerful, ESD-tolerant, robust, 5V-capable inputs and outputs). A tiny handful of 3V3, low-current IO are not particularly useful for realistic use-cases. Heck, even the Beaglebone, with its 1 GHz Arm A8 and 512 MB RAM has a pair of separate microcontrollers ("PRUs") for real-time IO on the SOC.

I wish there were some higher-speed, lower-level local busses for communication with subprocessors and other IO (SPI, CAN, etc), but Ethernet is fine.