Would be cool if Microsoft just changed all of their system storage to library-based systems, so you could have an Applications library that aggregated folders from across your hds.
Indeed. The trouble is that a lot of advanced users are more comfortable knowing the physical locations of their data, while casual users aren't informed enough to properly utilise such a system. It's one of the reasons the Library functionality introduced in Windows 7 hasn't really taken off. I consider Storage Spaces to be the better technology and that should be enabled by default, as that would protect against the failure of any single drive and it allows multiple hard-drives to appear as a single drive in Explorer.
Well, when using WinRT apps, you've kinda got that already.
Sadly, not many WinRT apps yet.
The trouble with WinRT apps is that the are hugely limited in terms of functionality and there is also a requirement to distribute them through the Windows Store, which means giving 30% of revenue to Microsoft. That's not an issue for mobile-style app markets but it's bad for the traditional PC software market, which is used to being open and flexible. For WinRT apps to take off Microsoft is going to have to expand the APIs considerably - including a 'full power' mode for desktop systems so that unlimited numbers of apps can run in the background - and allow for software to be distributed through third-party app stores (à la Android).