Found this forum when searching for my own info about playing lossless files on a iPod, so I figured I would chime in on this topic. I went through the same research process as you have when trying to decide what format to use to "archive" my CD collection, although admittedly I did not go as deep into the listening tests. I already had most of my CDs in iTunes as MP3s, but I wanted to redo everything in lossless format.
I ended up deciding to re-rip all of my CDs in WAV format. I understand that FLAC is a lossless format and therefore a FLAC file and a lossless WAV file will sound identical. But my non-expert opinion is that lossless WAV is an identical bit-by-bit "copy" of the original CD, so why not start there? There is no compression whatsoever. I used an older computer to build a NAS device on the NAS4FREE platform and ripped the CDs directly to the NAS storage; I run a Subsonic server on the NAS which allows me to stream all of my music in the uncompressed WAV format to various devices. The setup works great and the sound quality is spectacular! Perhaps I wouldn't notice a difference if I had ripped to FLAC, but since space is not an issue my thought was "why compress at all?"
My search now is to find a way to sync the uncompressed WAV files to an iPod so I can take the music in my car. In the alternative I figure that I can still convert the WAV files to another lossless format if necessary such as FLAC or OOG, in order to get them to an iPod. But I will always have the original WAV "archive" of all of my CDs. (There are Subsonic apps available for both Apple and Android devices and I have streamed WAV directly through a device to my car, but the larger WAV file sizes does sometimes cause pauses in the music based on the "current" bandwith in use - streaming WAV is fine if I am on WiFi, but streaming through my wireless carrier when away from WiFi is an issue).
Any suggestions or comments about how to sync WAV or other formats other than MP3 to an iPod would be most welcome! Even if it means no iTunes (which I would actually prefer)!