Just to let you know this is not dead. This weekend I worked on the code that will run on the MCU. The code is made to be easily ported from one Atmel to another, lots of "defines" and conditional compilation. In fact one only needs to alter the file "customize.h" to make it work with an other MCU, and even that is made to be easy. The code also implements an bidirectional communication protocol - or to put it in the usual RS232 words: I implemented an AT command set

The brave ones of you might want to download the code (it's in the attachment) and give it a try. The code is NOT complete: only one "dump" method is implemented, the code wasn't tested on anything but the Axon - in fact if you try to compile for an MCU that only has one USART you'll get an error because I haven't implemented that branch of the conditional compilation.
This is a quick reference on the "AT" command set, just to get things started:
"AT" => gives an "OK - I'm here message"
"AT?" => gives information on all available AT commands - sort of like an help.
"ATI" => gives information on the MCU and it's capabilities. It's designed so an GUI like the SoR Scope may parse the returned information and figure out what's on the other side of the RS232

"ATDUMP DECIMAL ALL 8BIT" (or it's short form "ATD D A 8") is basically the equivalent of the "axon_daq" - it converts and dumps all configured pinx (16 on the Axon) and writes the result as a decimal value (human readable). This is the only "dump" variation that works at the moment.
Right now the code doesn't work with the SoR Scope GUI (funny thing, isn't that) because the SoR Scope needs to learn to send the AT commands. The code is provided as an AvrStudio project: unzip, open it up in AvrStudio and hit "build all". I didn't provide an HEX file because I don't want people tempted to use it on the Axon with Axon's bootloader: This project was made from scratch, it doesn't include any of the Axon source code and I'm not sure if any special configuration options need to be made for it to work with the Botloader!
Anyway, have fun with the code, I know I had fun writing it.
More next weekend.