Have you looked into Amarra for iTunes?
As you saw yesterday, I'm with you on both the good and bad of iTunes. I tolerate it for now because it's free and my AppleTV (playback device... for now) was 150 bucks, as was the 2TB drive when I bought it. But the way it tries to force habits on me drives me crazy. The newest version won't even let me un-check "sync music" without giving me a dialog box that it's going to delete what's on the AppleTV. That's preposterously stupid. If my external drive isn't plugged in, I don't have the local storage to hold anywhere near what the AppleTV holds, so it's not possible for me to keep everything local too. And why the hell should I have to?
I plan to hack the appleTV so that I can use the external drive instead. I wonder how that'll affect the auto-sync crap.
I can't say I've had any problems with iTunes for ripping, or Apple Lossless as a format. I have an equal mix of M4A and FLAC, and for now I have all the flac duped in m4a as well.
I'm looking into what kind of interface/control I can get for an Auraliti player, as that intrigues me. I want to try one of those with a Peachtree Nova side by side with my Nakamichi gear to see if it blows my stuff out of the water the way I expect that it might. But a major consideration for me is integration of the controls into my distributed A/V, as I have a Crestron Prodigy setup that I've worked tirelessly to install over the past year and I've become very attached to my all-in-one iDevice apps. I don't want to have to toggle to another app if at all possible. I'm anal like that.
