The more I look at the differences between iPhone and iPad apps, the more I have to ask if a universal binary makes sense. They may both run on the iPhone OS, but the interface will be very different between the two devices in most cases. Look at Apple's examples like Contacts, Calendar, YouTube, Mail, they're totally different from the iPhone version. Even full-screen apps and/or games have a problem because you're going to want much higher-resolution textures for the iPad. Do you really want all the people who are only using the iPhone version to be required to download those large textures that they won't even use (which may well no longer fit inside the 10 MB limit for 3G downloading)?
What I'd like to see instead of (or maybe in addition to) universal binaries is the ability for a developer to link two or more apps in the app store, so once you buy one, you can download the other(s) for free. An extension of this that would be great is to link multiple apps into discounted bundles.