Work is being done on all of this, for sure.
The vanilla Qubes OS install is what we know is tried and tested against bugs and known vulnerabilities, fairly stable, albeit a little clunky and janky, sufficiently usable, reasonably idiot-proof (important for beginners), and we are willing to put our name behind it.
But I promise you, there are a lot of things out in the wild that have been added onto Qubes OS by the community.
Honestly, I’m not quite sure how cloning qubes impacts your ability to compartmentalise things. That’s a bit of a stretch, to be honest. But I suppose it would increase the storage requirements, processing requirements, memory requirements, etc…
It’s done because there are quite a few users out there that need that level of certainty that there’s no way that the process can be exploited by anyone (journalists, security researchers, “Dave from Finance”, etc.). Hence why it’s still the standard.
But I do agree with you that there are benefits to be had from “delta templates” or “snapshots” if you will, if done right, with no compromises as far as security/integrity goes.
It would allow you to stack multiple templates on top of each other, before you overlay the qube. You could even have a single application in a template, and overlay that application (and all it’s /lib, /etc, /usr, and /opt files) across an OS template, allowing you to (potentially) hot-swap the application onto a different OS, with all its configuration intact.
Yes, there’s a lot in this that can go wrong (trust me, I realised more the more I wrote it), but that’s the point that I’m trying to make. The devs have definitely thought about cool ideas like this, realised the fact that a cool idea takes a lot of time to become a solid one, and have opted to keep it simple, and build incrementally from there.
For every solid idea, there are at least 30 other cool ideas of a Qubes dev’s machine, in various states of functionality 
Side-note:
If you (or anyone reading this) have any code, by all means, commit it. Even if it’s broken, problematic, “not your best work”, or whatever. At least it will get the ball rolling for the community 