What's missing is legislation to level the playing field; either allow alternate stores on equal terms, or abide by rules that force you to play fair in your own store, things like that. There's no going back to the 90s, it's just a whole different world now.
Remember how when an older relative would complain about their computer slowing down, and you had to uninstall like 15 toolbars from their Internet Explorer?
Protecting users from malware and spyware is a huge step forward. Most users can't protect themselves from it. Controlled distribution is a net good for society. The question is, how do we minimize the negatives it also brings along with it, such as seemingly arbitrary, inconsistent, and/or vague rejections?
It's not about what we would personally prefer, as smart tech people who know how to protect ourselves. It's about what's best for everyone -- the societal good.
The conversation is about app stores not hardware upgrades.
Progress in one has nothing to do with progress in the other.
Why are you trying to combine them?