WOW! That is an amazing theory, Gaffer Tape! In your version, Luke would have been truly alone for the first time. Han is captured. He can't trust Obi-Wan and probably Yoda. Also, he is uncertain about his father and Darth Vader. I actually had something far less elegant in mind.
My theory was that Darth Vader would make the big reveal that Obi Wan killed your father in ESB, and ESB would end that way, with lots of uncertainty much like the normal one we are used to. The audience would be left wondering what the revelation meant exactly. Does it mean that Obi-Wan has been a villain all along? Did Luke's father turn to the dark side? Is Vader lying altogether?
Episode VI would have taken place right after Empire instead of a couple of Years after. In Episode VI, Leia, Chewbacca, and Lando would have saved Han in the beginning of the movie without Luke. Leia would be the leader of the rescue operation and no longer become a slave girl.
Meanwhile, Luke would fly back to Dagobah, eager to confront Yoda and Obi-Wan. When there, Luke would find that Yoda has passed away. He would become furious then find Ben's ghost standing there. Obi-Wan would explain that Luke's father had indeed fallen to the dark side of the force, along with Obi-Wan's padawan: Vader. Along with the emperor, Vader and Luke's father committed the purge of the Jedi, with help of the clones. Only a few Jedi survived, including Obi-Wan, Yoda, and Mace Windu (finally his character actually does something). Obi-Wan, the more powerful Jedi, can't bring himself to confront his apprentice. He goes and duels with Luke's father and sadly kills him, on Mustafar (as shown in the prequel trilogy). Mace Windu confronts Vader but fails. Mace dies but Vader is maimed. He gets put in the suit and is saddened when he hears Luke's father, his friend, has been killed.
Luke reluctantly accepts this truth, as he senses it to be true. Leia is not Luke's sister. When Luke, Leia, Han, and Lando regroup with the rebels, they find out that the Empire has been simultaneously and secretly constructing two smaller versions of the Death Star. There are currently two of these small Death Stars, which are not as powerful as the original but have the power to kill all life on a planet's surface (but not actually destroy the planets). The rebels decide that it is finally time to invade the Imperial capital on Coruscant. Han (with Chewbacca) and Lando go to destroy the two Death Stars; each one takes one Death Star. They spend the majority of the movie, trying to destroy the Death Stars. They eventually manage to get in one of the Death Stars and Lando stays to pilot it to crash into the other one. Han Solo says goodbye to his friend and leaves. Lando dies as the two Death Stars crash.
Meanwhile, Leia and Luke go on a mission to invade Coruscant. Luke's mission is to assassinate the Emperor and also unlock the gates that bar the main part of the capital where all the Imperial officials are. The control to unlock the gates is in the Emperor's throne room. He morally debates whether it is ethical to use his Jedi powers not for defense but to assassinate someone. He becomes conflicted and confused. He rationalizes the planned assassination by hating the Emperor.
Meanwhile, Leia invades the outer part of the capital and tries to hold it until the gates can be unlocked. Luke is able to gain access to the throne room but finds Vader and the Emperor awaiting him. He confronts Vader, saying that he knows the truth, and they have a duel as the Emperor watches. The Emperor proceeds to insult Luke's father and calls him a disgrace and a failure, as Obi-Wan defeated him. Luke becomes angry and uses the anger to defeat but not kill Vader (though Vader loses his hand). He has almost fallen to the dark side of the force just like his father. Luke looks at Vader's hand then at his own mechanical hand. He drops his lightsaber. He won't turn.
The Emperor is angered and begins shocking him, as in the movie. The Emperor is telling Luke how he is a failure like his father. Vader then hears the voice of Luke's father, Ben, and Yoda and realizes that he owes it to his dead friend to save his son from the dark side. Vader then takes his lightsaber and is about to strike the Emperor, in Luke's defense. The Emperor sees this and starts shocking Vader. Vader still manages to strike the Emperor down. The Emperor does not disappear, as he belonged to the dark side of the force. Vader collapses with his life support system permanently damaged. Luke consoles Vader as he dies, glad that Vader has turned back to the light side of the force. Vader's body disappears, showing that he truly redeemed himself and Luke. Luke then manages to deactivate the gates to the inner capital.
Leia leads the invasion force into the inner capital and captures the Empire. The Rebellion has won once and for all. At the end of the movie, Han and Leia are married. Luke is shown to be forming a new Jedi order. They have a celebration on Coruscant and the force ghosts of Luke's father, Obi Wan, Yoda, and Vader appear.
So there you have it. That was my mega theory to how the different twist would have lead. On second thought, maybe since I am asking for where the alternate twist would lead, this thread should be recategorized into Script Re-Writing. Moth3r, if you want to move this thread, I fully support your decision.