>"Well, I should be able to keep the OS and applications completely segregated from each other."
That's what VM's are for.
Upgrade your hardware, upgrade your OS, install and configure the VM, copy some files, and you're running the legacy OS and application again.
Eloquently put. OS X's move to sandboxed and self-contained apps is a step in the right direction.
And I want a pony.
Thank you sir! Hopefully someone hears about this, though I doubt it'll get resolved in the next decade, or maybe two if ever.