The $99 fee is basically the same as what it costs to become a developer for the iPhone. The $50 fee for being listed in the official App Catalog is different, and feels like a good alternative to me since they also have the free distribution option. This should help avoid the App Catalog getting over-crowded with a ton of really poor cheap/free apps, and hopefully means the App Catalog will attract developers producing the higher quality applications.
I think you are right on the effect. I bet a developer who hands over $50 will be a lot more uptight in delayed deployment of that app.
My main problem with the iTunes App Store from a customer point of view is I feel like I have tunnel vision and can't really see the app and comments. I wish I had something like the Amazon shopping experience.
