I can see where you're coming from. However, I think that scene was more about Luke realizing that fighting Palpatine with force (see what I did there?) would be useless-- after all, he was the only guy in the galaxy that could shoot lightning out of his hands. I like to think he put down his lightsaber and let the Force be his guide; and also let all that sweet talk he'd been throwing Vader since Empire Strikes Back finally pay off.
Also, I think Anakin did turn out to be the "Chosen One." He brought balance to the Force by letting the only real Jedis left die of old age then killed the remaining Sith. I don't doubt Luke eventually grew into the real McCoy, but in the formal (i.e. recognized) sense of being a Jedi, Luke was pretty much a Padawan.
One last thing, to whomever said that "but he was a self-trained Jedi" muck-- Yeah, okay but I'm not letting a self-trained doctor perform a heart transplant on me. There's a reason Jedi had a training system and it was to keep a higher portion of Force sensitives from turning to the Dark Side than just letting them experiment with the Force on their own (tell me if you were a child with the Force you wouldn't use it constantly to get whatever you wanted-- Dark Side for real). Without formal training, Luke can still call himself a Jedi if he really feels that way (plus as a state-labeled terrorist organization, that'll probably go over really well) but it doesn't make it so.
Luke and us (the audience) didn't know Palpatine had lightning (assuming you watched the O.T. first). Heck we didn't even know he could use the Force or his capablilies. Also Luke is a Jedi because he had the training, sure the training had to be adapted to the enviroment but there were no formal facilities at that time. Obi-Wan and Yoda also both trained him and told him that he was a Jedi.
You are correct Anakin is the Chosen One, George Lucas said so.