I completely agree with you, which is why my highest-level comment in this thread suggested using a new ISA, too. However, for practical reasons, it would be a ton of work to design and build hardware and a complete operating system. That’s the holy grail, of course, but it’s going to be hard to achieve without a large company backing it up.
You're missing the point. If the only goal was "functionality," a quick-and-dirty hack on top of existing systems would suffice.
However, the GP wants a system that's reasonably comprehensible all the way down, so he can have some confidence that it's not working against him in some way. The accidental complexity of decades of legacy software works strongly against that.