I'm not saying canonical is perfect or that they always make good decisions, but Here's a breakdown of why their decisions were made:
When ubuntu was first started gnome was the simplest and easiest desktop around, so they based ubuntu one that since it fit with their goals. As time went on ubuntu and upstream gnome began disagreeing about how to better the gnome desktop, ubuntu wasn't able to get indicator's or notify-osd accepted upstream because they didn't fit with gnome's vision of the future gnome 3, so they added the ayatana patched to their gnome 2. When gnome 3 came around canonical and gnome further and further disagreed on how to do things, but canonical still heavily depended on gnome for the desktop, so they wrote their own unity shell and continued to use gnome underneath.
Now its clear that canonical and upstream have very different ideas on how to do things, so it is in canonical's best interest to completely break from gnome and write unity in QT/QML (QT/QML is also straight up technically superior too IMO, and I am a gnome user). I think this is a smart decision given what they are trying to do. No one is forcing you to use ubuntu anyway.