I've had my iPhone for almost two weeks now and I absolutely love it. It's the best cell phone I've ever used and the sexiest gadget I've ever owned. But there are a few things about it that really, really suck:
iTunes is the only way to transfer music, photos, movies, or anything else to the phone, and the Windows port of iTunes sucks donkey balls. It's slow, ridiculously unstable, and completely ignores standard Windows UI practices. If it were possible to sync my iPhone by letting Chuck Norris kick me in the crotch, I'd choose the crotch kick over iTunes any day.
No native IM app
There are a few good Ajax IM apps for the iPhone, but they're all severely limited by the fact that they can't provide audio alerts and only work when Safari is the active application. As soon as you switch to another app, lock the phone, or even look away from the screen, they become useless.
There's no way to email full-resolution photos
The 2 megapixel camera on the iPhone is decent and certainly usable for casual photoblogging via Flickr, which is something I've been doing for years now. Unfortunately, when you email a photo from the iPhone, it sends a tiny 640x480 version of the photo rather than the 1600x1200 original. There is no way to change this.
This means that in order to get my full-res photos on Flickr, I have to dock the iPhone, copy the photos over to my computer, and upload them to Flickr manually. That's silly. Even my ancient Nokia 6600 from a few years ago could email full-resolution photos to Flickr.
The calendar won't sync with iCal feeds
Despite the iPhone's excellent Internet capabilities, the calendar app can't be synced with iCal feeds over the 'net. Just like everything else, the only way to sync the calendar is to dock the phone and fire up iTunes, and even then it will only sync directly with iCal, Entourage, or Outlook.
I primarily use Google Calendar and Windows Calendar (which comes with Vista and happily syncs with Google Calendar) to manage my schedule, but the iPhone won't sync with either of those, even though they're both capable of publishing iCal feeds. On Windows, it will only sync with Outlook, and I don't use Outlook. Lame.
The fact that the calendar app is otherwise very good makes this omission suck even more.
No Ogg Vorbis support
I know, I know. iPods have never supported Ogg Vorbis, so why should the iPhone? Truth be told, I didn't buy the iPhone for its iPod functionality; I bought it for the phone and Internet functionality. But it's so damn good at playing music that I've stopped using my trusty old iRiver H120.
The only problem is that all the music I've purchased in the last two years is in Ogg Vorbis format, which the H120 supports very well. Now I have to convert all those Oggs to MP3s if I want to listen to them on my iPhone. I'm not sure what Apple has against Ogg, but I sure wish they'd get over it.
It may sound like I hate my iPhone, but I don't. I love it. I want to have like a million of its babies. The fact that I love it in spite of these major drawbacks should tell you something about how awesome it is.