The vast, vast majority of 'regular' iPhone users have never, and will never hear of the apps described in this post. For them, the default apps are just fine.
That's not to disparage the choice, just to recognise that regular users don't care about this kind of thing one bit.
The thing is, not everyone will customize all apps, but everyone will customize at least one app, be it a better todo list, a better IM, a better picture-taking app, or a better recipe database. Which is why the appstore is so popular.
EDIT: clearly the "regular users" I know are different from everybody else. The North of England must be a hive of phone-geeks living in some sort of bubble.
Everyone will customise their experience of the device, by adding what they like from the store.
My point is that, more often than not, these users won't replace core apps like Mail or Calendar - these apps work just fine for most people and there's no incentive to change.
Also, iCloud was announced in June 2011; plenty of todo apps had cloud sync well before that, when Apple simply didn't provide the service.