Hmm tough choice for me.
In general there is a lack of decent science-fiction RPGs so I really like Fallout 3, however Oblivion seemed to have a lot more depth to it, character generation options, etc.. plus I liked the way skills go up over time as you use them.
I'd rate them as being more or less even, but give it to Fallout 3 simply on the merits of being a science fiction game, despite lacking the sheer array of stuff to do in like Oblivion.
Frankly though I think Bethesda has been dumbing down it's games too much. Originally they were sort of famous for their mature content, now they seem to be focused on making everything and everyone seem fairly dumpy, and freaked out over fan-made nudity mods for Oblivion. On top of this they have been reducing the number of options involved in their games, for example you could not fly accross the landscape in Oblivion like you could in Morrowwind which I personally found very annoying, they also reduced the number of factions/guild you could join, as well as the overall number of skills.
That said, with the Fallout 3/Oblivion thing resolved I'd probably have to say that the best RPG in the series was Wasteland or Fallout 2. >
Fallout 2 simply had so many things to do in it, and was jaded in ways that no game has yet been. While Fallout 3 was a great game, I think Bethesda should have launched it's own franchise without the name since while it's a great game it's just not a true "Fallout" game. The old Bethesda could have done Fallout, the new one (attitude wise) couldn't quite pull it off.
Wasteland which was arguably the prequel to all things Fallout let you both create your own party of four AND recruit guys for your team. It had a decent number of skills, and several differant ways through most of the problems in the game. While technologically primitive, especially by today's standards, it also included a free-roam enviroment where you could go anywhere including walking into an area substantially more powerful than you are and getting waxed.
Ultimatly for a true RPG I like to be able to create my own team, rather than at the most one character. Sadly very few games do that anymore. Thus I feel that allowing for it's age "Wasteland" is the best game remotely connected with this discussion.