For those apps that have both an iPad version and an iPhone version, I agree, they should just have one Universal iPhone/iPad app, even if the two apps are fairly different in functionality due to the screen size/UI differences. However, as a developer, my first iPad app simply won't work on the iPhone as the interface doesn't scale to a small screen well (or small keyboard for that matter). I won't be making an iPhone version separately or as part of an Universal app.
Edit: On second thought, there are cases where I don't think this is true. If an iPad app really takes advantage of the bigger screen, it may end up being much more complex than its iPhone counterpart, justifying a higher price. It's not really fair to make users who only ever want to use it on the iPhone pay the higher price. However, in that case I think a higher-priced Universal app (for iPad and iPad/iPhone users) along with a cheaper iPhone only version makes sense.
Edit: On second thought, there are cases where I don't think this is true. If an iPad app really takes advantage of the bigger screen, it may end up being much more complex than its iPhone counterpart, justifying a higher price. It's not really fair to make users who only ever want to use it on the iPhone pay the higher price. However, in that case I think a higher-priced Universal app (for iPad and iPad/iPhone users) along with a cheaper iPhone only version makes sense.