What you're describing is the situation every time you develop on someone else's platform: Apple's, Microsoft's, Facebook's, everyone's.

If you're developing apps for a platform you want to be in one of two positions:

1. The app is secondary to whatever service you're providing (eg the Facebook app on iOS); or

2. You're developing games.

Everything else has to walk a fine line between failing and being successful enough that it gets absorbed into the platform.

Apple is just like everyone else in this regard. No platform owner is going to ignore something that they decide has become of critical importance to their platform. It's simply a fantasy to assume otherwise.

If you're not in one of those two categories you're basically hoping to be the lucky one who gets bought out (eg the official Twitter mobile client).