Split View: If you have an iPad Air 2, you can use Split View instead of Slide Over to read emails and view other apps side-by-side. Need to copy and paste details from Notes into an email to the boss? Split View is perfect. (Though you could presumably do that with Slide Over, too.)
Picture in Picture: For those times when you have to get work done but your parents really want to have a FaceTime conversation (or you want to catch up on Last Week Tonight--no judgment), Picture in Picture is a great new way to multitask. You can move the picture around and resize it so it doesn't block the email you're trying to read (or write), but it always remains the top window.
iOS 9 didn't dramatically change the Mail app at its core, but little tweaks and systemwide multitasking tools make email slightly less awful to manage.
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