Jsh1120, I guess I'm confused (no sarcasm, I really am confused). How is managing your applications using a media player a problem? What difficulties are you experiencing? I'm sort of late to the party.
I think you're not alone in being confused. Apparently, there are several discussions and sub-discussions going on here. Let me
try to clarify. I'm not promising to be successful.
() My reference to iTunes as a "music player" was rather imprecise. Originally, iTunes was an application designed to enable computer users to buy and play songs. It has since morphed into other kinds of content but the basic interface (on a computer) has remained largely the original design. It works well for managing the content on old iPods (like mine) but becomes increasingly confusing and inadequate as one moves to iPods (i.e. Touch) that run apps, the iPhone, and especially the iPad where songs are likely to be the least important content type. Yet the iTunes application (and even its name) suggests otherwise.
() Apparently, (and not surprisingly) the iTunes app runs better on Apple computers than on Windows systems. I can't comment on the former because all my systems (other than the iPad) are Windows systems. This issue morphed into the (somewhat unrelated) issue of how it runs on Vista and the awful problems that afflict that OS. Suffice to say that problems exist even with Windows 7 systems. The issue of whether anyone should suffer with Vista is a separate one and extends far beyond the issue of whether iTunes works well in that environment.
() Some of the discussion apparently confused the "App Store" app on the iPad with the iTunes application on a computer (which is what you deal with when you sync your iPad.) I happen to think that the App Store app is also lousy mainly because it is so difficult to search for specific apps. Many folks agree with me on that score which is the basis of some posts that point out the value of App Shopper when you're trying to find a specific app. In any event, the quality, good or bad, of the App Store is a separate issue from the quality of iTunes as an interface for managing/syncing apps and media content.