He is the Chosen One, but he is not all powerful. Hell, in Attack of the Clones, Anakin was only a simple Padawan, and he was exhausted from fighting beasts and robots and whatnot in Geonosis. How the hell is he going to turn around and fight a Sith Lord with decades of experience after ALSO getting hit by powerful and damaging force lightning?
In Episode 3, you have to also consider that Obi-Wan was older and had more experience than Anakin. Anakin likely would have won the fight, but Obi-Wan took the high ground (which he so eloquently explained) and was able to take advantage of Anakin's arrogance (arrogance being a common trait of the Sith). I don't think that there would be any question that Anakin would have won otherwise.
As for Episode 6, the fight did seem strange, but you have to consider that Luke was the SON of the Chosen One. He may not have had as high a midi-chlorian count, or have been as powerful with the force, but he was still an incredibly powerful Jedi Knight. Hell, Cade Skywalker was able to devastate Darth Talon despite having much less experience with the force. Palpatine's continued taunting, and Vader's comment that he would turn Leia to the dark side, simply sent Luke over the edge. He came out at full force, with the strength of rage and the dark side behind him. If you watch the fight, he's not even battling very gracefully. He swings his lightsaber around like a club, and Vader keels over until Luke finally chops off his hand. My theory is that Vader felt exhausted (he was a middle aged burn victim with 3 prosthetic limbs in a heavy respirator suit), and he knew that defeat was inevitable. He simply fell to the ground with exhaustion and hopelessness.
As for The Force Unleashed...screw that shit.
