First off Thanks for making the Luigino328. I love the concept and picked up two of the protos. I am not worried about the ICSP being off. That's no big deal as there is a good workaround.
I was looking into placing a Luigino328 within an enclosure but the mounting hole placement is off. I'm alright with only having three holes but they are off a bit and the proto boards will not work in any enclosure setup for the standard arduino mounting hole layout .
The second thing is the automatic serial port selector will also disconnect the "external" TX and RX if the arduino IDE serial port monitor is brought up. I noticed this when I was working on debugging my serial prints to an LCD board and then brought the serial port monitor up. I'm not sure if this is intentional or just the way it will work.
Anyways. Thanks for making the arduino better and I'd be happy to evaluate the final version once it's completed.