I'm in the same dilemma picking between AU SIS and UCSD IR/PS.
From the three people I've asked so far, the two "practitioners" - a diplomat and a think-tank director - seem to favor SIS. My advisor, on the other hand, places UC San Diego over American academically, going so far as saying UCSD is ranked higher than American as an IR school. There is obviously a gap between how these two groups view programs.
In my opinion, UCSD is definitely the better place if you still have a PhD in the back of your mind; it is more highly respected by academics. Moreover, specifically with regard to connections and opportunities in East Asia, it is not certain that American is better than San Diego. IR/PS also seem to offer a better combination between a professional and an academic future.