Overall, Duo-R's probably the best setup for most people if you're going to just keep one system. Style wise, I think the Duo-R is middle of the road amongst all the PCE variants, but that's just personal opinion (still better than TG16+CD setup, though).
Functionality wise, the Duo-R trumps the TG16+CD. It's easier to maintain, repair, get parts for, better compatibility (not just with wide selection of games, but with periphrals such as controllers, etc), TG16 can't use arcade cards without a mod, etc, etc...
About the only reasons to prefer the TG16 setup might be for nostalgic reasons, or if you HAVE to play US cards and you don't want to mod the Duo-R (which you must do in order to play US games.)
To add the cherry on top, you'll probably get more cash for the TG16 setup than the Duo-R setup.