I get what you mean, I wouldn’t want it to be an assimilated project like that either. The question is, will Unity7 have enough maintainers to be on its own safely, especially considering that relies on compiz, something that mid-to-long term will be considered obsolete as wayland becomes more and more common.
Then again, I don’t see xfce, for example, using anything other than X for a long time.
I do know that my comments are from the perspective of a user exclusively. I’m not into the technical details and I won’t pretend otherwise. That said, I see what you mean regarding nautilus from a user’s perspective, and makes me think of nautilus vs. nemo: even though I use nemo for myself, I don’t really advise anyone on my family to use it with standard Ubuntu 16.04, as nautilus feels more responsive and stable, so something must be going on under the hood. caja is equally stable and responsive as nautilus in my experience though, but I’ve always imagined that’s because it’s been very consistent since its fork from GNOME2.
What I’m trying to say is that whatever you guys decide, I do know it’s with that balance you speak of in mind and it will be the best possible technical decision. 
