Well Apple doesn't force you to use iTunes to manage and organize your music library. It provides an option in iTunes to allow you the freedom to tweak your library as you wish. It is quite easy to drag and drop any files from your music library into an ipod. You don't have to create a second copy of your library to use iTunes any more than you need to create a second copy if you use windows explorer to drag and drop files into your DAP.
I'm more sympathetic to your point about the different types of encoding that are used. To be honest, I was confused for quite some time over the many types of encoded files out there and trying to decide which ones to use.
The good thing is that there are some good conversion programs out there like dBpoweramp that make that task relatively easy, if you decide to go with another file type.
I'm not going to manage an iPod by drag and drop. I have over 600 CDs. That's not going to work. I need to be able to use playlists and smartlists and keyword searches and tag searches and fancy database expressions. Drag and drop would be doable with 60 CDs, it doesn't work with 600+ CDs.
Maybe the new round of DAPs based on Google Android will finally give me something reasonably close to what I want. Will they have gapless? Will they sync properly using third-party media players/managers? They'll still end up including too many features that distract from the primary function of a DAP, but as long as it plays and manages audio properly I can deal.