Sill replacements can be done and still use an insert window.

Not saying one is better than the other, but I want you to understand that a sill replacement does not mean that you need to go full tear out on the removal.

Good point, some of the jambs from the bottom (lower corners) do have problems also, and I want them all to match, so I don't think I can pick and choose which method for what window.
Also, there is one window that is a basement egress window that is in a concrete surrounded area. It has rot through to the framing. Can't go bigger, and we're already on the edge with the egress limit. So I'm not sure a full frame replacement (slide-in) will work there.

Believe me, I don't really want to remove the whole window, down to the RO if I can help it.

Let's assume for a moment, that I could salvage the existing frames, what is the best quality replacement option if I want clad w/ wood inside, and in DH?

Capping will even out and cover all the wood rot replacement and provide a seamless look to the opening.

Marvin Ultimate, Pella Architect, Jeld Wen, Andersen, etc all make a wood clad insert window.