Siloing data on a per app basis isn't going to be enough for things like photos -- there's just too many files. We've all heard your arguments before about tags & search vs. folders but in the end it comes down to the OS and the apps that run on it providing good defaults for folders and/or tags and helping the user keep their files organized in some fashion. Shifting from folders to some other organization technique doesn't necessarily solve the problem.
But files/folders doesn't help any more there either. So most people stick with one tool (be that Flickr/Facebook/Picassa) and use that to organise their photos. How it ends up being stored on the computer is basicallly irrelevant as far as they're concerned. And a tool deliberately aimed at organising just one thing, i.e. photos, is always going to be better capable than a tool aimed at generic organisation, i.e. the filesystem.
And for the record I disagree with you're presumption that re file systems that "end users often find the concept quite confusing". There are just as many who find it useful. Also there is still a file picker in metro that relies on the file system so it's not going away any time soon.
For every one person who finds the filesystem a useful concept, there are easily several thousand who don't. It's a very low-level metaphor and one that is a long way behind the times. I've spent years dealing with end-user support of PC systems and this is one of those areas that consistently causes problems. For first time users of computers (and there are still plenty) it's a horrible experience and it's one of the things that makes devices like the iPad a lot more appealing to the masses, because that "just works"
Even the file picker in Metro mostly abstracts the file system away by doing things like constraining the amount of browsable locations and only displaying things the app can understand, preferably in an appropriate format. It pushes closer to the direction of picking where you're pictures etc come from in the user's mental model (i.e Facebook, Flickr, Picassa etc) rather than some arbitrary filing system you thought up a few weeks ago and can't really remember.