The problem is, there's a easy way around paying Apple the initial distribution fee if they make the IAP cut less than the app purchase cut.
Option A: I sell an app for $10, Apple takes $3 for hosting the app and future updates, I get $7 that covers development and maintaining any other content it needs to download.
Option B: I put the app on the App store for free, and charge either a $10 subscription or in-app purchase to unlock it completely. The burden hasn't changed on either party for who distributes what, only when money changes hands.
If Apple took less of a cut for In App Purchasing than buying the initial app, there's a loophole where everyone would just give the app away for free, and use IAP to unlock it later. For a popular app like Kindle or NetFlix, the $99 developer fee probably doesn't cover the distribution costs alone.
The current compromise is somewhere in the middle.. Apple eats the cost of distributing these apps, but doesn't do so in a way that results in everyone giving away free apps to skirt the App store cut.
The better option might be to allow developers to opt in to a lower transaction % cut, but pay for the distribution costs. Instead of 30%, pay 4% on IAP + $0.20/GB or so whenever someone downloads your app or an update. However, that's no where near as simple as the current mechanism.
Part of the problem here would be charging users for an app that was previously free. Unless it's some super-duper Pro/HD version of the app with a heck of a lock more functionality. So you then force users to upgrade, or lose out on features.
People baulk at 99cent apps, so if you were to suddenly charge ten bucks for it they would be seriously annoyed. Plus you would get seriously crappy reviews for suddenly putting a price on a previously free app.
As for the second option, I'm not sure if IAP guidelines allow you to do this. I think subscriptions cannot be used to unlock an app, they have to be recurring and not one time, so what, a yearly fee? hmm, interesting, but as said, pretty sure you cannot use subs in this way.
Your suggestion about a lower fee instead of the 30% would be fantastic, but it's not going to happen. Apple knows full well what it is doing, it knows about the 70 / 30 split, it came up with Agency Pricing. It's plan is to try and kill off all ebook apps bar iBooks on iOS, and on that score it is doing a tremendous job, which is very unfortunate, especially if you happen to work for one of the competitors.
Oh, and in case the review I mentioned goes missing (seems it's not appeared on the US App Store yet, probably won't either), have a read of it
here. It explains some of the behind the scenes things that app developers have had to go through to deal with the new guidelines.
