This has been in the works for some time, but I have a working proof of concept now. There are two shields (RPUftdi* and RPUadpt**) and two microcontroller boards (Irrigate7 and an Uno clone), they share the serial interface over the CAT5 cable to a host UART, which is on the RPUftdi shield. The RPUftid shield is on the ATmega328p board, while the RPUadpt is on Irrigate7*** (ATmega1284p).
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http://epccs.org/indexes/Board/RPUftdi/
** http://epccs.org/indexes/Board/RPUadpt/
*** http://epccs.org/indexes/Board/Irrigate7/
An idealized view of the CAT5 wire usage.
A quick video shows the bootload of ATmega1284p.
Related firmware is on Github*. RPUftdi management MCU has Host2Remote, while RPUadpt management MCU has Remote. The bootload firmware uploaded to Irrigate7 is BlinkLED.
I probably need to say that the firmware is makefile based, and the goal is to be able to build and upload from a Raspberry Pi using a command line SSH connection.