Before I go into the imperfections of the iPhone, I must mention that the iPhone is one of the best (smart)phones I've had so far.....My (smartphone) references are the Nokia Communicator, Nokia E61i, Nokia N95. While the PDA experience comes from Psion (to bad that they are gone), and a boatload of crappy/unstable Windows CE/Mobile platforms over the last 10 years.

Every device had its limitations, but the iPhone clearly has the upperhand (at the moment). But there's always room for improvement :-)

Sounds

You can add (custom) ringtones, but no notification sounds for e-mail, and other messages.
No way of changing the default e-mail message tone.
Really annoying, since several collegues have an iPhone, and they all have the same new e-mail message tone.

Profiles

No idea how the caal it, but it's nice to have several notification/presence profiles on the iPhone. You only have;

Sound / No Sound
Vibrate / No Vibration

Now I have to adjust my ringtone volume on several occasions. Outdoor maximum volume, while inside I have to trim it down a little.

Disk Access

No place to stuff potential downloads, or transport (drag) files on your iPhone. iPods have this capability, why doesn't the iPhone.

Calendars

I use the corporate Exchange 2007 calendar, but I also have an iCal on my machine at home. You can't merge them, because they won't sync to iCal after that. So you have to work with two calendars (if you want to seperate work and personal life). No problem if you could move/copy calendar entries between the different calendars. Every once in a while an appointment ends up in the wrong calendar.
Now I move them the Chinese way.... Take all the details on one of them, enter it in the other calendar and remove the original.

Contacts

Awesome that you can browse the corporate directory when you use Exchange 2007, but there's no way of directly selecting or searching this addressbook from within the Mail app on the iPhone.

Also, if you receive an e-mail form a collegue, there's no link between the senders address and the entry in the corporate directory. So if you get an e-mail and want to call the person back, you need to remember his/her name and look it up in the corporate directory.
Same goes for the telephone numbers. No link between an incoming call and the number in the directory.

Syncing over the air

The iPhone has wireless AND bluetooth capabilities. Why do we still need a(n overpriced) cable to transfer synchronization data between the phone and PC/Mac (read: iTunes)?

I don't want to use the MobileMe platform unless they have a Calendar and Contacts only version only for a dollar a month with 100MB of space. I don't need the webspace, or iDisk space. Just call it SyncMe Lite.

Additional iPhone Thoughts