The Witcher blows TES out of the water for me. The storytelling and characters are far more superior in TW and TW2 than any other recent RPG I've played.
But, as mentioned above, it really is apples and oranges. Most people in this thread are probably going to say TES is better, and that's okay with me. Oblivion has such a boring, generic fantasy storyline to me, which doesn't really help the game along.
The Witcher also has a much better morality system than any other RPG I've played. It's not your standard "Oh look, Commandor Shophord, you can choose to be good, neutral, or evil, herp derp." Rather, there's no good or bad. Everything is a shade of grey. There are some parts of The Witcher that will really make you question your morals. Not to spoil anything, but if you were given a choice between supporting the game's equivalent of Israel (Strong army repressing others to ensure their civilians live comfortably), or Palestine (stripped of basic rights yet use terrorism to further their cause), which would you choose? And which friend would you kill for the other?
Until someone can show me an RPG with writing as phenomenal as The Witcher, it will still be my favorite RPG series.