Make it easier to delete message en masse: On the iPhone, there's no easy way to delete more than one email message at a time. Combine that fact with the iPhone's lack of any sort of junkmail filtering, and deleting all those email offers for low-priced medicine and penny stocks becomes a repetitive – literally - drag.
Let users mark all messages as read: Just as the ability deleting messages in one fell swoop is missing from the iPhone, so is a way to mark all messages as read. It shouldn't be.
Force messages to display as plain text: Many people dislike HTML-formatted email. Spammers use it way too often, image-heavy messages take a long time to download, and, quite frankly, many pre-made HTML message templates are just plain ugly. On your Mac, you can use a hidden Mail preference to force all messages to display in plain text mode. That preference is missing from the iPhone -you're stuck with a veritable barrage of image-laden and slow-to-load HTML messages.
Add more flexible options for selecting text to be quoted in replies: We've already noted that you can't select text on the iPhone; that goes for replying to messages, too. You have no control over how much of the original email gets quoted. There's also no setting for enabling or disabling quoting in general; Mail on the iPhone automatically quotes the entire message when you start your reply. Adding these capabilities would be a big step toward making the iPhone's Mail even more like its OS X counterpart.
Make picture-sending easier: If you have a series of photos to send off to someone - pictures of the kids, say, that you want to share with their grandparents -you're going to have to send a series of emails. You can only select one photo at a time; a multiple selection tool would make things much easier.
Allow images from emails to be saved to the Photos app: Photos received in Mail are stuck there; you can't add emailed images to the iPhone's Photos application - at least not easily. You could move the photos into iPhoto on your computer (if you're a Mac user), and then add them to the iPhone the next time you sync, but this is a capability you should be able to do entirely from your phone.
Enable custom ringtones: Most modern phones let you add custom ringtones - simple melodies or even actual music files. Some phone providers require you to purchase these ringtones through a service, whereas others let you simply upload the ringtones directly to your phone. The iPhone does neither; in fact, other than assigning different built-in ringtones to particular contacts, the iPhone offers little in the way of ringtone customisation.
This may seem like a frivolous feature, but it has practical purposes. For example, you can assign a meaningful custom ringtone to a specific person in your contact list so you know when that person calls without even looking at your phone. Plus, custom ringtones are just plain fun.
Yes, there are several unsupported solutions for adding customised ringtones, but they don't let you use iTunes Store purchases and they're... well... unsupported. It would be nice to have an Apple-sanctioned, fully-featured method to do what many comparable phones already allow.