Note: This is conjecture, as I was unable to find canon references to back it up.
When Luke leaves the first time, he is told that he could possibly help his friends, but would put all they've worked for in danger. Being the feckless youth that he still is, he charges off anyway, loses a hand and Han. While confronting Vader at that time was dramatic, it was still just a fight.
During VI, Luke helps rescue Han, then returns to Dagobah. At that time, Yoda confirms that yes, he is Vader's son, and that there is another Skywalker. The spirit of Kenobi confirms that it is Leia, and Luke tells Kenobi that there is still good in his father.
The final confrontation is not only just Luke vs. Vader, but Luke versus the Emperor, and Luke versus himself, which is arguably the most important. As Luke chops off Vaders' arm, he realizes that he is on the path to becoming the same as his father, and "wins" his self battle by casting aside his weapons.
It's more a battle of self realization and triumph over internal doubt, which he didn't really accomplish in the battle in Cloud City.