There are two issues that are coming up here: sandboxing and paid upgrades. They are quite different. As a consumer I am completely for sandboxing for myself and for other consumers. In a world where malware is increasingly a problem sandboxed apps will become the norm. That's the reality we live in. Sandboxing being a requirement means that I can fairly safely install anything from the (future) Mac App Store. The OP…
It's not that simple. Arbitrary features of your favorite app may not be allowed on the App Store just because Apple didn't feel it worthwhile to create an entitlement for that feature. Everything they add has a cost and it's very easy to say "that's not important."