In my opinion, Apple should just do what Windows does with downloads, and warn users when installing unsigned apps. This provides the best of both worlds. Keep charging for the privilege to sell on the App Store, but please, just let me use my device how I want to.
* Apple still charges $99 for a developer license/kit
* Apple still runs their AppStore
* Apple releases specs/API for creating your own AppStore
* People create competing AppStore implementations
* By default, Apple's AppStore is the only one configured
* The interface for adding extra AppStores is a bit hidden and rough around the edges, so that people have to be motivated to actually do it. (i.e. raise the bar a bit, so that the people that do it know what they are doing)
The majority of people would still just use Apple's AppStore, but this would allow Apple to side-step the "We can't approve that because it would be bad for our company image to have it in our AppStore" type of issues. Apple could even void the warranty for people that use competing AppStores as a way to raise the barrier, but at least it would still be there for the people that wanted to use it.
Would I like to be able to use more crazy, non-standard , non-Apple-approved software on my iPhone? Hell yes! If I were Apple, would I allow others to distribute software for my device? Hell no!
If I had created both the device(s) and application market, I certainly wouldn't let other people compete with me in my own business -- that's just foolish, especially since the current business model works, and works well. Appeasing a minority of highly technical users doesn't make sense in this market.
Besides, how is Apple's model different from what set-top console makers (Nintendo, Sony, Sega, ...) have done for years? $99 is cheap for a console development kit; since you must have Mac to run it, it'd be about $700 total for a development kit + Mac Mini -- and that's still inexpensive in the console devkit market. It's a unique niche, and I'm more than happy to pay to play in it.
I think the solution is just to allow anyone to install an alternative "unlocked" OS on the device. You'd have to jump through some hoops to do it, but once you did you could do as you pleased (and give up your right to any support from apple). Basically allow jail breaking w/o the need to find an exploit to do it.