The first complaint is the click wheel is really not that great an operating device. It took me a while to figure out the various ways this worked. There's a "Menu," back and forth arrow, a circular motion, a center button, and "play/pause." The circular motion does different things depending on what menu you have. In play mode, it's the volume. In menu mode, it cycles through the menu. Sure, fine, I can get used to that. Except for the worst part about this navigation tool: it is far too sensitive and had no tactile feedback. So my thumb or finger slides around a featureless smooth plane, which means I have to look at it or "guess" the distance based on how far my thumb and finger are from the edge. My thick thumbs have a tough time staying within the printed lines like a toddler with a jumbo crayon, and often I can't select what I want without staying perfectly still. It's like operating an old ball mouse over a table with crumbs on it.
Not only that, but having the player in my pocket or any enclosed space changes things at random. Yes, I even bought a protective case for it. Yes, I can lock the wheel to not move at all, but the lock is a thin, hard-to-grip button at the lower edge (especially with the protective case over it), so have to remove it from the case to slide it back and forth. Plus it locks everything down, so if I use it, I am unable to change the volume or anything, which means to suddenly hear what announcement is being made over the Metro or if someone starts speaking to me, I have to quickly yank out my ear plugs. Then there's my music which doesn't have a steady volume for each song, plus I'll need to change the volume from "drown out the city traffic" to "be polite and not irritate people near me with tinny techno beats on a quiet metro ride." I have had enough times where I had needed to hit a "mute" of sorts that I never lock down the volume/pause, and so I have to be careful I do not bump the face of the iPod. When walking, this means in my pocket will often raise or lower the volume, and click back and forth between songs randomly. I think the best solution would be to get a set of headphones with a mute built into the cord.
The second gripe is iTunes. I hate iTunes. It has made my Windows boot time nearly 3 minutes from the 55 seconds it used to be. Can I drag and drop music? Oh no... I have to let iTunes load it, and then it wants to scan everything else, and thanks to my iTunes, I now know I have 9800 songs on my shared drive, which it wants to reload any time I add music. Not to mention it wrestles to be the default media player, and then doesn't play the music I click on right away. Sometimes I have to double click a song several times to get it to go, "Oh, you want to play something! Sorry, how about renaming it instead?" It always seems to be "working in the background" in some way. I see it taking up to 150mb of RAM at times, take up 10-30% of CPU when loaded, and ... oh, won't let me play or load ogg files (I found a hack to let iTunes play it, but my iPod refuses to acknowledge it). Plus iTunes only uses Windows. I am going to give Banshee a try on Ubuntu, though.
An annoyance I have for all MP3 players I have ever had: Time left and skip ahead for podcasts. I want to know how much time I have to go before the end, in case I want to speed things up before I hop off a stop, or find a good place to pause. To find where I am, I have to fast forward or reverse to get that bar. Plus, I can only fast forward or reverse about 10 seconds per second, so if the iPod resets my placeholder to the beginning for various reasons, I have to remember where I was, and hope I wasn't in the last 20 minutes of a 2-hour podcast, because there's no "rewind from end" feature, only fast forward from the beginning. So if I got reset at 1:00 in a 1:20 podcast, it will take me nearly a minute to get one hour forward into the podcast.
I am not sure the iPhone will be much better (as a music player). It does not have a click wheel, but it's an all-screen interface. The headphones do have a mute feature, though, to answer calls. That will be REAL handy. My biggest fear with an iPhone? How to carry it around while using it. It's a bit big for a belt clip, and I am afraid as much as I run into things that I'll break the iPhone in a matter of weeks with it attached to my hip.