I am unfamiliar with Yamahas product, so can't say. But, a quick look just makes me wonder how scalable of a product it is. Would you want to add more functionality, is the MP3 server your primary listening, or is FM good enough - or XM radio. It looks like it may be a fair bit of coinage for the MP3 server, plus you need to get wiring/power to those wall units somehow. If you are in the midst of construction it may not be an issue... But, if you are in the midst of construction I would wire the heck out of the home and look a lot more.
I have a digital music server w/Crestron distribution but most of the time my wife and I just turn on XM Radio for the continuous variety... or lack thereof on certain stations we enjoy.
For amps, there are tons of excellent manufacturers including Niles, Sonance, and others. I use Rotel for all of my distributed audio needs, but I use separate amplification for every room (RMB-1048 x 2)