On Tuesday during Apple’s Q3 2009 conference call, Apple COO Tim Cook expressed interest in what eventually could become a radical redesign of the current App Store available for all iPhone and iPod Touch users.

The idea comes just a week after we were discussing the very problem of having too many apps on the App Store and the difficulty in separating the good apps from the bad. With 65,000 and more application offerings available, many users only browse the Top 25 section of the App Store, completely ignoring any other amazing apps that may be diamonds in the rough. With the way the App Store is designed, navigation quickly becomes a burden and the Top 25 apps seldom change due to their popularity and ease of access.

However, most of the congestion in the App Store comes from the thousands of Apps that cost only $0.99, as apps at that price point are much easier to purchase than any other price category. But this itself is an inherent problem.

As more and more applications flood the App Store, and as the customer base for the App Store grows, prices will naturally reduce over time. The problem here is that there will be a point for many developers where making a high quality application will become unreasonable because the development costs will far outweigh the proceeds. Moreover, if a high quality application is released for $0.99, there is a large probability that it may simply be lost in the sea of bad applications.

There is no doubt that Apple needs to redesign the App Store and give users more control over their purchasing content. Giving customers the ability to download a trial version or “lite” version of the app is one strong idea, but ultimately more than just a mere trial version will be required, especially in terms of navigation.

When asked about the App Store, Tim Cook responded:

“As you know, today we do it by type of app and also have show popular apps and top-selling apps, et cetera. We realize there’s opportunity there for further improvement and are working on that.”

With that statement, iPhone and iPod touch users may see the needed redesigned for the App Store, but a time frame is unknown at this point.