I keep checking this thread to see how the Armalite is progression.
Yea, there has been some stagnation while we wait for the Due. With the strength of the brand, and probably a good deal of work on compatibility, the Due may have a lot of clout and it may be very valuable to be as compatible as possible. Or it may flop.
Do you have any idea yet about the likely price range? Over $100 or under?
Your points about the I/O limitations of the SAM3 cause me to wonder how the Arduino team will deal with that. If they come out with a board which physically fits the shields, but can only source and sink a pitiful few milliamps, at 3.3v or below, then there could be a lot of confusion among the target audience.
I kinda like your approach of starting afresh with a new daughtercard interface; and possibly supplementing that with Arduino shield compatible sockets for backward compatibility.
I'll probably go for the raspberry pi eventually, but yes I do see a different niche. While some degree of ecosystem will evolve around it with stronger IO, I'm not yet clear if anybody will be supporting an environment lighter than Linux on the RPi? Good for some things, not so good for others.
Anyway, I'll keep checking on your progress.