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You're right. I work full time on Facebook Applications and there are several things hindering the FB Platform. First is the lack of moderation of apps. Secondly, the approved advertiser list has too many companies promoting mobile offers (which are spammy) (http://developers.facebook.com/adproviders/). As a consequence Application ads are seedy. Think 'You have 1 new message' type ads, or "Are you smarter than Obama" type ads. Thirdly, the whole Permissions/Authentication system needs to be improved. The Permissions wall in its current embodiment advertise the negatives of adding an Application.

Even if you disagree with the above, you should agree that an API that accounts for 10% of a site's traffic, like Facebook's, is a struggling ecosystem. Src: http://www.businessinsider.com/facebook-news-feed-apps-2011-...