From what I've been able to gather, the design principle behind the menu is that only application-global state (e.g. "About" or "Settings") state should need to be accessed from there, so in theory you shouldn't need to hit it very often.
Certain applications break this rule, with annoying results: for example in Empathy (the default chat program) much of the key functionality is only accessible from that app menu. So all of a sudden when I want to add a contact I need to use this menu that I would almost never touch otherwise, which is awkward and annoying.
I think much of the complaining about Gnome Shell is just grousing, but I have to agree that the global menu stuff seems pretty poorly thought out. It's completely different from what everyone else does, yet it's not well documented or obvious how it's supposed to work (I only found out about its rationale after being curious about what they were thinking and running a few searches through Google).