The guy is a great engineer. Great engineers don't invent great things, they build great things - most of the time, using shitty things as experiments/prototypes/proofs of concepts in order to get the great thing done
Yes, an engineer which is great when you're dealing with computers. But a desktop is essentially dealing with humans which is a completely different problem set and I would say a lot harder. In GNOME, it takes an enormous time to get all the details right on a user interface. It is nothing like working with a kernel. It isn't as easy as you think it is. Even the early desktops took all their designs from Windows 95, copying a lot of the look and feel because nobody was trained on how to write a user interface. Even today we're still messing around with the same design.
I suppose you're just asking Linus Torvalds to re-engineer windows 95 interface, I suppose he could do that. But to do something new, and unique that requires an anthropologist.
There is not only an app store concept that is being developed, but also a sandboxing mechanism for better safety when you run your apps. On top of that, you should be able to use apps that have older libraries and so forth using a system that Lennart Poettering has come up with. Again though, we do have to change Unix cultural for some of these things.
Right now, we need to continually upgrade ourselves otherwise, it will be Android that wlll be the desktop of choice on Linux machines. In fact, even the identifier 'Linux' will be gone, nobody will even know that they are running Linux since FSF can't seem to come up with something better than 'GNU/Linux". *sigh*