From what I've seen, the Duo-R's seem to run a bit smoother regarding CD games, they just seem to tick along nicer.
If you get a regular Duo, it will need a recap, unless of course it has already been done. Not that much of a big deal if you know someone locally that can do it, but it is an added expense.
They do differ (the regular Duo vs the Duo-R) internally so it would be interesting to hear some opinions about the advantages/disadvantages of each design. I do tend to hear negative things re the original Duo beyond the original caps used, such as poor placement of components leading to a tendency for certain things to overheat.