I also have Mac+Itunes+WiFi+AE, but sound quality after update to Music is exactly the same. Perhaps something else changed?
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I didn't hear any difference with the switch to Music from iTunes with a similar setup in one system, iMac/WiFi/Airport Express. The optical output from the Airport Express and Apple TV suffers from a lot of jitter, timing errors in the digital signal. If you want to stick with the AE the biggest improvement you could make would be to put a reclocker between the AE and the DACs inside your amps. I've used a Wyred4Sound Remedy Reclocker with great results and there may be other such devices out there. An external DAC that does a better job of taming the jitter than the internal ones in your amps could be an improvement, as well.