There is actually no plot hole here. It really has nothing at all to do with Luke's fencing skills. (In fact, Vader may still have the advantage, though it is hard to tell since Luke basically handicaps himself, and Vader may not even be fighting to win. There's too much rhetoric for it to be a real fight to the death.) Consider the context of the quote:
(Luke fences Vader, kicks Vader down the staircase, starts to advance)
Emperor: (cackles) Good! Use your aggressive feelings, boy! Let the hate flow through you!
Luke: (powers off his light saber, faces Vader, exhales) I will not fight you, Father.
It is not Luke's fighting skills that prompts Vader's comment, but his ability to resist the seduction of the Dark Side. Even during what Luke believes to be a duel to the death, standing alone against two opponents likely stronger than he, and with all of his friends dying just outside the window, Luke still keeps at the forefront of his mind what Obi-Wan told him on Dagobah before he reunited with the fleet:
Bury your feelings deep down, Luke. They do you credit, but *they could be made to serve the Emperor.
And also Luke in this fateful moment still maintains his composure with Jedi discipline, as Yoda counseled him from his death bed:
Remember, a Jedi's strength flows from the Force.
But beware: anger, fear, aggression - the Dark Side are they.
Once you start down the Dark path, forever will it dominate your destiny.
Do not underestimate the powers of the Dark, or suffer your father's fate you will.
Obi-Wan and Yoda similarly counseled him as he was preparing to leave Dagobah for Cloud City:
Luke: But I can help them! I feel the Force.
Obi-Wan: But you cannot control it. This is a dangerous time for you, when you will be tempted by the Dark Side of the Force.
Yoda: Yes, yes! To Obi-Wan you listen! The cave - remember your failure at the cave....
Obi-Wan: Luke! Don't give in to hate! It leads to the Dark Side!
Even though Obi-Wan is only with Luke physically for about a day's worth of time before Vader kills him, Obi-Wan and Yoda have counseled Luke on resisting the Dark Side about equally, at least judging by what is shown on screen in the films.
Returning to the climactic sequence, another relevant detail is the reaction of the Imperial fleet command officers to the Emperor's orders for the Battle of Endor:
Admiral Viett: Hold here.
Officer: We're not going to attack?
Admiral Viett: I have my orders from the Emperor himself. He has something special planned for them. We only need to keep them from escaping.
The Star Destroyers could have just destroyed the rebel fleet themselves, but the Emperor personally ordered them not to. The Emperor also claims:
Everything that has transpired has done so according to my design. Your friends on the sanctuary moon are walking into a trap, as is your rebel fleet.
It was I who allowed the Alliance to know the location of the shield generator....
The Emperor seems to have orchestrated the entire elaborate ambush on the rebellion primarily in order to provoke Luke into rage and thereby seduce him to the Dark Side - with actually killing the rebels amounting to a bonus.
Emperor: Come, boy. See for yourself. From here you will witness the final destruction of the Alliance, and the end of your insignificant rebellion.
Luke: (looks at his light saber on the arm of the Emperor's throne)
Emperor: You want this, don't you? The hate is swelling in you now. Take your Jedi weapon. Use it. I am unarmed. Strike me down with it! Give in to your anger!
Luke: (gives a mocking look, turns away)
Emperor: With each pulsing moment you make yourself more my servant.
Luke: (breathes heavily, turns back) No.
Emperor: It is unavoidable. It is your destiny. You, like your father, are now mine.
Emperor: Your fleet is lost. And your friends on the Endor moon will not survive. There is no escape - my young apprentice. The Alliance will die, as will your friends. Good... I can feel your anger. I am defenseless. Take your weapon. Strike me down with all of your hatred, and your journey towards the Dark Side will be complete!
This scene in Episode VI, and Anakin's conversion to Darth Vader in Episode III, indicate that at least when Sidious is involved, provocation to rage is a critical element in converting a Jedi to the Dark Side. The Jedi must lose discipline and indulge in anger, fear and aggression, and in doing so make himself vulnerable to the domination of his new Master. But despite the combined efforts of Vader and the Emperor, Luke maintains composure under intense pressure, even to the point of powering off his saber in the middle of the fight.
It is this very high level of discipline that causes Vader to compliment Obi-Wan. Because Obi-Wan tried, and failed, to teach Anakin those very virtues, but in Luke's case, along with Yoda's help, Obi-Wan has not failed this time. By heroically resisting their provocations, Luke defies the Emperor's foresight and remains a Jedi.
With this quote, Vader gives credit where it is due. I even perceive in this statement by Vader not only an admiration for Obi-Wan, that Luke is so well trained in his mental discipline, but also an expression of regret, that had Anakin been so well prepared himself, that he would never have been seduced by the Dark Side to begin with.