iMessage needs to actually work with contacts. Apple needs to work out how to unify email address/phone numbers somehow so that multiple message threads don't occur. Its confusing especially when you end up reply to the wrong one and the recipient doesn't receive it on their iPad etc.
Simply changing the caller ID isn't ideal as you still end up with 2 threads if the sender only has your phone number. Its an awful messy system that is ruining my family and friends experience.
FaceTime needs to auto detect contacts that are able to receive FaceTime calls and auto add into the address book. Similarly ios devices should show up correctly labelled in the address book.
Apple should REALLY stick it to the Phone Providers by allowing VOIP - i.e. the iMessage of calls - wifi only of course! added into the phone seamlessly.
It also needs siri to work in the UK. Its embarrassingly useless and doesn't understand my average southern accent.
iPhoto needs to not look horrible. I can't believe it was allowed to be released looking so tacky. It also needs to replace photos at some stage and work seamlessly syncing between the OSX version.
Documents need to sync with no user action. A simple toggle at the top right of pages/numbers (in OSX and iOS) should sync the document with iCloud, and likewise remove it.
Dropbox is incredible. Apple need to either integrate it within all OS's/Buy the company out or think up a suitable cross platform (i.e. windows) rip-off.
iOS needs to be able to airplay music to MULTIPLE airport extremes at the same time.
Geobased reminders DESPERATELY need improving (like somebody already mentioned). You need to be able to pin point the location on a map instead of having to enter an address in the address book.
I'm sure they are waiting to release their new apple maps/satnav thingy for this though.
Reminders need to sync directly with OSX for them to be useable. Currently I have to use evernote which is OTT and clunky. I think snow leopard should resolve this though.
What has struck me as the result of everyones replies is that apple needs to play some serious catchup, or as soon as people start becoming bored of apple and the sparkle wears off, they will become frustrated at being strung along every release.
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There's a list of many hundreds of things I'd change about iOS, but the most important thing is sorting out it's file management so you can get data on and off the device more easily. There is absolutely no reason iTunes should be involved in this process - user data should mount under USB, bluetooth file transfer should work, I should be able to organise my photos into folders and not have them appear in the camera roll, I should be able to upload files via the web browser, and apps to upload and download data should be able to access other applications files.
It is *crazy* that we have the current situation. It makes iOS so hard to use.
Phazer
Whilst I understand your personal need - I used to work the same way years ago, I don't think iOS is for you. It will never work that way as thats not how your average consumer functions.