Last time I stayed at the Commander, I made the reservations by phone to SPG because I was using a SPG50 and the woman on the phone reserved a smoking room for me for some stupid reason. Well, I'm a repeat customer, so the staff was a bit confused. So they had reserved both a smoking suite and a non-smoking back corner room (349) for me and let me pick, and said that they'd have a non-smoking suite for me the next morning.
I decided after about three minutes that I liked 349 just fine. It is about 10% smaller than the junior suites, but still a good size for somebody like me that likes to pace. The room layout was better organized (you could actually see the TV from bed, for example) and it didn't have the canopy bed which I find kind of annoying when travelling alone. I'd still prefer the junior suite, but 349 isn't bad.
A great thing about the Commander is that they take the SPG50s most of the time. During low season there's no point, but during high season it saves about $40-$60/night on base rooms. Since you can find SPG50s easily "for a good home" in Coupon Connection, it's a nice deal. And if you don't have status, the SPG50s get you into the junior suite (called an "executive king" on the web site) for a reasonable price.