I think most of the arguments about iTunes is just because it's a different way of organizing your music than folks that have owned other players are used to. If you already have all your stuff organized in playlist folders on your disk and you just want to copy that to a new iPod, you're going to have to do extra work to get it working again.
Once you get over that, I think that having all the tag data accessible in iTunes and on the iPod makes it much better once you get over the hump of not just using folders on the drive to organize your music anymore.
The only times I even look at my music files anymore is when I back them up
And I dont miss messing around with poorly or incorrectly labeled files, sorting irregularities due to spelling errors, multiple copies to have it in multiple playlists... etc.
This particular computer engineer doesn't mind not having to mess with the individual files anymore at all. Never looked back since I got my first iPod. Give the non-files/folder way of organizing it a chance and you wont regret it, unless your mp3 files or whatever dont have the tag info embedded properly as is often the case with files you downloaded...