Some of the issues stem from a tendency of Gnome to want to "manage" your stuff for you. Evolution sticking its fingers into other things, something indexing files, apps wanting to manage your photos. I've had trouble with my music collection. You'd think it's possible to copy some folders with .mp3 files into your home directory and point the music app at it. But no, files have to be imported or some crap and I actu…
As a result, many apps ended up feeling like a pretty thin veneer around a file explorer. My memory is a little foggy, but the music player and the email app come to mind.
The opposite model was the iTunes model: a monolithic app that reproduced a bunch of functionality of the file system, but ultimately nerfed the power.
I’m otherwise not too crazy nostalgic about BeOS (NeXT was the better OS in many ways). But man, some things were really great with that system.