Parts of what you are saying are interesting and I am not against something like that. But it seems that the direction Apple is headed is in apps being self aware of file types that relate to them as apposed to the user doing the work like in archaic file systems.
If they do expand in this area I would be a bit surprised. I think they have many other things on their radar prior to what they have already designed as such. I wouldn't expect anything in iOS 5. The big thing I am hoping for is a new notification system and continuous client type integration between iOS devices, Macs with 10.7 Lion, and a new MobileMe. I think those are safe bets!
I agree that apps do and will be aware of the files they can use. But each app is a silo and for heterogenous filetypes this is a problem. Images are dealt with by the image library api, but it's a limited api and doesn't handle all the other filetypes out there. You can't even share data between applications created by the same company. Secondly, you only have to look at the pages/numbers & iTunes filesync UIs to realise they are interim steps, they do not scale and don't allow you to pull files from anywhere other than their filesystem sandbox.
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