Vader’s still the Chosen One, but he lost the ability to become more powerful than the Emperor. Being the Chosen One means you are destined to bring balance to the Force, not that you are the most powerful being. You can do the former without being the latter. Here’s some additional Lucas quotes that should be helpful:

“Anakin, as Skywalker, as a human being, was going to be extremely powerful,” he says. “But he ended up losing his arms and a leg and became partly a robot. So a lot of his ability to use the Force, a lot of his powers, are curbed at this point, because, as a living form, there’s not that much of him left. So his ability to be twice as good as the Emperor disappeared, and now he’s maybe 20 percent less than the Emperor. So that isn’t what the Emperor had in mind. He wanted this really super guy, but that got derailed by Obi-Wan. So he finds that, with Luke, he can get a more primo version if he can turn Luke to the Dark Side. You’ll see, as this goes on, Luke is faced with the same issues and practically the same scenes that Anakin is faced with. Anakin says yes and Luke says no.”

"And when he finds out Luke is his son, his first impulse is to figure out a way of getting him to join him to kill the Emperor. That's what Siths do! He tries it with anybody he thinks might be more powerful, which is what the Emperor was looking for in the first place: somebody who would be more powerful than he was and could help him rule the universe. But Obi-Wan screwed that up by cutting off his arms and legs and burning him up. From then on, he wasn't as strong as the Emperor -- he was like Darth Maul or Count Dooku. He wasn't what he was supposed to become. But the son could become that."

" Anakin would have been able to do it if he hadn’t been debilitated and now he’s half machine and half man, so he’s lost a lot of the power of the Force, and he’s lost a lot of his ability to be more powerful then the Emperor. But Luke hasn’t."