No subfloor should not be a surprise in a 100 year old house. This was pretty common practice, particularly out in the country and there was a lot more country in California 100 years ago than today.
There are several ways that you can go, Ross. The easiest would be to just refinish the present floor. If you like the wood that's there, go ahead. Be prepared for some gaps between the boards and don't try to put filler between them. The boards will always expand and contract and more across the width so any fill will just crack out eventually. A nice touch would be to add fiberglass insulation between the joists in the basement but use unfaced. This will stop drafts. The faced insulation might be easier to install but the vapor barrier that is formed could cause you problems with humidity later.
In my opinion, the better solution would be to use the current floor as a subfloor and install a hardwood or engineered floor. I would bet that your current floor is out of level and your best bet would be to have an experienced pro do it.