Hi there, you may remember me from many years ago at the LCA Arduino miniconf giving a talk about XMEGA internals.
There were a few key decisions I made when I started a design for an XMEGA-based arduino clone. These are the things I look for in improved or changed features from the standard official boards.
#1 - Conflict-free additional hardware.
I really hate it when a board adds additional features but overloads the shield pins. Okay, the extra hardware is nice but if it takes away IO pins from the shields and there's no way to disable it, then it makes the shield IO a bit useless. It's already hard enough to sort out what pins shields use without half the IO pins taken oven by on-board hardware.
For some stuff, this is easy.. SPI devices just make the !CS pin not one of the shield IO pins and have it pulled up by default. LEDs other the D13's LED belong off the shield IO pins, same goes for rotary encoders sensors and whatnot. I2C have some straps you can cut if you want.
#2 - Use additional IOs if they are there
The additional flash and RAM of the newer MCUs is great, but given you've got the spare IOs you may as well use them. This folds into point 1.
#3 - Decide if it's a close cousin or a completely different board.
I really hate the Leonardo pin-out, and the fact SPI is now "officially" from the ICSP header rather than D10-13 where it was. I2C is sort of overloaded on A4/A5 because that's where it was on the 328P but there are now dedicated I2C shield headers. Okay, well, it's a bit of a mess, so either decide you're going to follow the Uno pin-out closely or not at all, and document what the variation is. (IMO, PWM is about the only thing which I think is okay to vary, otherwise please stick to common usage!)
#4 - The shared USART
A few times I've run into people who are surprised they can't have separation between the shield USART (where, for example, you'd whack GPS or GPRS shields) and the PC/console USART. 1284P has two of them, please split it so they're now no longer shared!
Okay, what about the JTAG port etc. I know most people don't use it, although it's very cheap to get something to debug with it (ie, the AVR Dragon). That said, if it was a choice between #1 and JTAG, I would choose #1 every time, and I don't get the impression many Arduino people do JTAG anyway.
On the power side, well I'm biased towards switchmode. I put together a switchmode input shield (http://nicegear.co.nz/arduino-shields/w ... r-arduino/
) kit precisely because I think either you're better off with a variety of beefy 5V sources (in which case, just lose the 5V reg entirely), or do it properly for wide input.
Anyway, that's my rant. YMMV. Shall be interested to see a 1284P variant, I had considered for a long time building one myself after the chip became available but.. hobby vs job.