We'd love to be able to mark everything in a mailbox as read; delete all messages in a mailbox; flag messages (and have that status synced between devices); send to contact groups; save attachments to an area accessible by other apps; and have more control over text when viewing and composing messages. We'd also like to see a few desktop-inspired features such as mail rules and smart folders (ideally synced from OS X Mail), multiple signatures, folder editing, and local spam filtering. Finally, we hope to see Mail's two-pane view when the iPad is in portrait orientation.
Our wishlist is probably long enough as it is, but we can think of a few more iOS improvements that defy categorization.
: For a device that can do so much when untethered, it's still frustrating how many things you do wirelessly. The most obvious example is syncing data with iTunes, which still requires a physical connection. But there are plenty of other things relating to data we'd like to be able to do wirelessly--for example, instantly sharing a URL or a bit of text from your iPad to your computer (or vice versa) or sharing a Google Maps route from your iPad to your iPhone. There are third party apps that handle some of these things, and you can sync other types of data if you've got a MobileMe subscription, but imagine if your computer and your iOS devices kept close tabs on each other, making it simple to share and sync data instantly.
: Far more than the iPhone or iPod touch, the iPad has turned out to be a device--everyone in the family has a favorite use for it and wants a turn. While iOS provides a number of ways to restrict or allow particular actions or access to certain apps, the iPad's version of iOS would do well to provide more options for multiple users and finer control over app restrictions.