The orignal OpenROV design used a custom-built cape for the BeagleBone that did, indeed, have an Arduino Uno design on it. The current software is designed to be backwards-compatible with the Cape, though at last report there is some bug with downloading new code to the cape.
Here at OROV HQ there are no plans to change from the Arduino Mega on the current controller board. The added RAM and I/O on the Mega are extremely useful to us.
The schematics for the original Uno-based cape are on GitHub. If you want to experiment with using an actual Uno board, feel free! We always like to see people trying new things with the ROV hardware.