IGN had some suggestions in an article the other day as to how to clean up the App Store. I have some too.
First of all updated games as IGN stated, should not be brought back up to the top of the "new games" category. I don't think there should be a spot for recently patched/updated games either. A developer shouldn't be able to update their games infinite times to get it back to the top of the new games list. Although that may help with longevity of a game it also hurts the market for other games.
You could get updates out to the people by doing the things they already do. The feature already in place where Apple pushes out the update to the buyers to tell them there's a download ready is one method. The other, which is already in place too, is how iTunes tells you when an Aoo has updates available.
Second of all, visual appeal of the App Store. Not just visual appeal but information and how it's posted.
Apple would be smart to make fewer icons visible on at least the specialized sections if not the main page of the App Store too (but arguably that's where you want lots of Apps getting publicity rather than a select few, making it more a corporate matter than an independent one because the guys with the money would be the only ones to have space up there.
On the "what's new" section up top they should have three lines of apps rather than two-showcasing 12 apps rather than 8- to maximize on the space they use. And I don't really see the need for the "what's hot" section. The "what we're playing" section is a good one, if they can find a way to elaborate while taking up no extra space that'd definitely be cool.
The top middle section should widen each of the three icons a little bit. One should show a trailer of the newest or 'hottest 10 apps of the week' and the other two should be open for advertising.
I don't believe I've seen trailers for any App on it's App Space, just screenshots. That needs to change fast.
The charts along the side should still have the best seller list for paid and free Aoos but it should also have Top Rated Apps (with 10 reviews or more).

Uchiha_madara