I've said it a million times: Why do fanboy
Star Wars stories have to involve: a major SW character and/or the revival of the great Sith and/or a problem which AFFECTS THE FATE OF THE ENTIRE GALAXY!!!!111 ...again.
Also, yeah, let's just take the fictional universe continuity made by professional writers and throw it out the window! It doesn't matter, that Luke Skywalker faced Palpatine and Vader, probably the most powerful Sith lords ever, and essentially defeated them both! And then Darth Stupidname
pops out of nowhere with his little fan club of wannabes, and is able to kill Luke Skywalker. Right.
"You are an extremely powerful sith you can fly"
- sounds like The Matrix
. Just like Darth Stupidname, from under what rock did this super-Force-user appear?
I would say, tone down the "super-uber-leet" scale of characters, take out the roles of Jaden and Luke... and instead of a great Sith lord, have the villain be a fallen Jedi student, or perhaps a renegade reborn. This would make it, so the story could be believable, and would fit in the continuity of the SW EU.
Many of your plot points are sound, even good... but the "super-ness" of your original characters, and your use of already established characters, ruins the continuity and believability of your story... which makes it much less enjoyable.
So, here are a few suggestions for revisions:
As far as the main characters, and the places of Jaden and Luke... why not make it, so the villain, had some personal connection to the main character and/or the supporting characters? Like they were friends at one time, and the villain fell to the Dark Side.
Let's say the main character has feelings for another Jedi student, who is under the same Master as the main character, and the three go off on a quest to stop the villain's evil plan, and/or to turn him back to the Light.
In the meantime, something happens and the main character becomes corrupted, and in the state of Dark side power, kills his Master, and joins the villain. (Basically, this would be in place of the fight with Jaden)
Then, after some time, the young Jedi who has some bond with the main character catches up with them, and duels the main character, but, having feelings for the main character and sensing the good in them, refuses to fight, and gets killed by the villian before the main character's eyes. (This would essentially replace the scene with Luke)
This would allow for the personal quest of vengeance with the main character versus the bad guy, which was a strong plot line in your story. Also, the new original characters allows for no problems regarding continuity, and believablilty.
Also, it would keep the good plotline of having the main character shunned by the Jedi Order (falling to the Dark side and being involved in the death of two other Jedi), and being enemies with the villain and his group, which puts the main character alone in a hostile setting.
If you still would like a fight with Luke, perhaps you can make it at the end, since the rage of vengeance would corrupt the main character again, Luke can appear to try to bring the main character back into the Order... but in any case, you can't have Luke killed. It destroys continuity, and also, who are you to think your story is good enough to kill off the MAIN CHARACTER in the whole Star Wars universe?
Anyway, you have some good plot points in your story, I would hope you would atleast consider revising your characters to make them fit better within the continuity.