I actually really like the idea of sandboxing and entitlements for Mac apps. It's appropriate for like 90% of all the apps I run and I'll happily click through a scary warning for the things I don't think ought to run in a sandbox.
For some developers the MAS is a really nice alternative to direct distribution. You don't have to setup a merchant account and deal with all that. Your apps are automatically searchable (if not really discoverable). You have a built-in review/rating system to establish credibility pretty quickly (which absolutely impacts sales). It's not a horrible system, and again, Apple doesn't force you to use it... unless you want to use iCloud, but then again there's nothing stopping you from doing your own cloud sync solution as Omni has done.