brad,
Legacy joinery is joinery from a previous life, and I didn't mean to imply that you can reuse the joinery in a new structure -- there are way too many variables to allow that to happen often. I will repeat that I think trying to regain strength by plugging old mortises is a losing proposition.
As for aesthetics, I have done it both ways -- filling the holes with carefully chosen color/grain/hewing pattern-matched dutchmen, as well as leaving the old mortises open. It's all up to the client.
Being a framer with a history problem, I like to be able to see the hand tool marks inside the old joinery myself. I can see how they did things and what tools they used, and it seems that I often see things I've never noticed before.
Tell us a little more about what your planning to build-- sounds like it will be fun.
gh
