It's a bit fatuous to assign blame to a license agreement. You can assign blame to people that choose license agreements. In this case, that's the VLC developers for choosing the GPL, and Apple for choosing the App Store restrictions. VLC was under the GPL long before the App Store existed. It's a bit silly to say that they chose this particular incompatibility. Apple when drafting their license terms probably did not even consider the GPL, but their choice of terms is, in actual fact, banning GPL licensed transactions from using the App Store.

Their rules are mutually incompatible.

Which changes nothing, as it still isn't a conscious act by Apple to explicitly ban the GPL.

The GPL banned itself from the App Store, plain and simple, yet everybody will still make it about big bad Apple censoring libre software from the App Store. You chose the GPL when you started your project, Apple didn't. If the license that YOU chose for YOUR software doesn't allow you to distribute YOUR software under Apple's EULA, that isn't Apple's fault.

There's also no financial incentive for them to modify their EULA to be more GPL-friendly. They're going to say, gee, those hundreds of thousands of apps on the App Store have succeeded with the EULA we have, why get into legal battles over two publicized apps? The publicity is negative for us, so why bother?

On the same basis the USA bans GPL software, you aren't allowed to export stuff to naughty countries if you are American. The GPL doesn't allow you to block Cuba so nobody in the US is legally allowed to use GPL.

This doesn't seem to led to IBM, Oracle etc stopping selling Linux. Apple put a line in it's\ EULA about only being able to use app store for non-commercial use, which is ridiculous businessmen do use iPhones and iPads