When I started bringing up the 1284p, Sanguino seemed dead. The last update was to arduino-0017 or some such. Didn't seem like a useful point of reference.
As to the analog pins, I wanted them to follow Uno convention, so that analog channel = digitial pin - A0.
Backwards compat is critical for people who want to re-use shields of course, but personally I have no use for it. I've long since stopped using shields (and 5V for that matter). Whenever I put a 1284 into something, it's a custom piece of hardware.
Plus back-compat pin mappings are horrible confusing on a breadboard. Anyway, Arduino encapsulates pin differences in 'variants', so it's easy to switch from one to the other.