It's funny -- when the iPhone App Store first opened up, the first thing I asked for next was a way to manage apps from directly within iTunes. But when that finally did show up, I was still left unsatisfied for some reason. I'm not sure why -- app management offers drag-and-drop functionality with your app icons, and that's about the easiest way to organize things across the home screens. But for me, it still seems unwieldy somehow -- dragging icons onto full pages stlll creates empty pages, and dragging icons between screens is awkward to me.
I'm not an interface designer, but having more than one home screen open at a time seems like it would be nice, and being able to assign my own tags and categories to apps (combined with an auto-sort function) seems nicer. Don't get me wrong, I appreciate that we can manage apps from iTunes, but it just seems harder than it should be.