I know that the question was about OS architecture but I really feel like the UX is not as good as it could be. One thing I've been thinking about recently is that it could be interesting if there was some GUI system that would follow the Unix principle of having many small, task specific applications that could be easily composed together. It happens to me a lot that there are 3 applications each of which does something better than the other 2 but in the end of the day none of them is ideal. If I could pick the best of the 3 and put it together myself, that would be great.

Later, I realized that Mac OS' Automator/Applescript might have been an attempt to do something like this but it feels somewhat half-assed. Given something like this is probably impossible to bolt on later so you'd have to design the OS from the beginning to allow for this.