adilinden:
That is what I was thinking too. The SPI and I2C port placement is more important to me then PWM or pin change interrupts. I noticed there is no TX LED for the USB interface. Also, I would imagine the bootloader would have to be adjusted to support different pin assignments for TX and RX activity LED's. I think it would be trivial to utilize any of the D22 through D25 ports to light up some LED's.
This was my comment to the Arduino team, but it seams that they though other way. It is strange though, considering that it is very easy to do a compatible logical mapping, i.e. hardware pins to what the SW knows them by. I wouldn't be surprised if they do it for their commercial release though (a bit of misdirection there to avoid having any clones out there before their official release?).
For the RX and TX I would maintain the pin assignment that we've used. This is used by the core and bootloader to blink the LEDs when sending and receiving information from the USB virtual serial interface.
I will have to learn how to tell the Arduino environment how the hardware is configured. I've had some very brief glimpses into the Arduino core files, just need to learn and understand them. How to build the bootloader is another thing to look at to properly support a different hardware configuration.
This is all in "hardware/arduino/variants/leonardo", very easy to change (not very elegant nor efficient but it works, though). Whatever you do there has to be done in the bootloader "pin mapping" file too (well you can get away with minor changes there.
I've changed the bootloader and it compiles just fine, no problems foreseen there.