For many people you're probably right. I do think that there's tremendous value in segmenting out one's various personæ. There's no particularly good reason why I should give a binary game blob access to the same user data that contains my financial data, passwords &c.
A finer-grained system would be nice, no doubt, but OS users are pretty time-tested.
> Maybe someone else here has already thought about it and can put it into writing?
Well, in principle capabilities systems can do a lot of this already. As myself, I can give a capability to a server, and it can use that capability to execute work on my behalf; once I've received the result, I can (presumably) revoke that capability. Capabilities can even be used to implement filesystems: my process might have a filesystem root capability, which permits it to see a single directory, which is itself a list of capabilities to directories and files, &c. Pretty neat stuff.
There's been some interesting work with capabilities done in EROS, its successor Coyotos & Tahoe-LAFS.
I skimmed your thesis—really interesting work!