Notifications for e-mail would be helpful and I'm surprised they're not present in the current version of the OS.
Rules for e-mail would also be great.
I'd also like to see more extensive use of data tags across applications.
More speculatively, I see can see the iPhone becoming a truly mobile computer so better support for higher resolution displays then is currently available via the A/V cable would be great as well as support for Bluetooth keyboards. This would facilitate more business related applications.
Perhaps a future version of the iPhone will be your computer. You dock it and its OS appears on the monitor.