First, Epic and Tim Sweeney suck, the way they have gone about this has been awful, and on principle they should be tossed out for how shady they have been through this whole process.
That said, it will be interesting to see what the court comes up with for a fee structure. They should have the information about what it would take to make the App Store profitable, and that's really a key factor...Apple has to make enough of a profit to support apps and a store, if they don't the whole thing shuts down. And, apps cost money at some level for all of the stuff Apple puts together to support them, even the absolutely free ones cost Apple in terms of software development, hosting, and bandwidth. Whether they are charging too much or not enough should become apparent after the court analysis...it will be highly amusing if the court determines that Apple should be charging more for the App Store and is absorbing some of its costs elsewhere, an outcome where Apple is told to raise its prices would be pretty ironic.
The argument over side loading shouldn't come into play for that part of it, that's an argument to open the iOS platform up to installations outside of Apple's control...there are so many bad things that could come out of it that the few good things for those of us that could do it securely really aren't worth it for Apple. Charges for in-app purchases should be looked at though...I'm not even going to try to guess at the most fair method for that, it's really complicated.
At least we'll get some closure on this soon, and perhaps this will then set a standard that all the other App Stores (including Epic's thing) can follow...we all know that other app stores are set up like Apple but have gotten a pass in a lot of this. The biggest question is if this benefits the consumer in the end...that's not why Sweeney took this on despite his protestations, and his ill intent just might turn out to cause more trouble for people once this is all settled.