Logitech Harmony 720
The Harmony 720 did the trick. This model is only available at Costco, I think; it's not even listed on the Logitech web site. It has the color LCD screen like the 880, but it's rectangular like the XBOX one, rather than that ugly peanut shape of the 880. Anyway, I'm sure most of the Harmony remotes will work the same.
After unsuccessfully trying to 'teach' the remote the IR code for powering on Zone 2, I resorted to the help pages of the Harmony software, where I learned on the FAQs that all you have to do is set it up in the remote as a second receiver. You name it Yamaha RX-V659 (zone 2) and the remote knows to send it zone 2 codes. So, unlike the Yamaha remote, the Harmony will stay in Zone 2 mode as long as you want, and will change inputs, control volume without affecting zone 1 at all.
I highly recommend the Harmony for zone 2 control. My zone 1 is the master bedroom, and zone 2 is the bathroom where I have ceiling speakers for music, so I just turn on the music from the bedroom and let it play. I don't need a second remote that stays in zone 2. If I did, I would get a RF Harmony remote.
I don't know anything about the other models that other posters have mentioned, so I'm not saying it's better. Just wanted to give another option that I can confirm works perfectly.