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Let me say first and formost Qui-Gon Jinn is my favorite character. Now let me explain why his character is one of the biggest flaws in the prequel trilogy.
The way I understand the story development of TPM, originally there was only Obi-Wan. This is the best scenario. At some point Lucas decided he wanted Obi-Wan to have a partner of sorts, so he created Qui-Gon. Qui-Gon evolved into Obi-Wan's apprentice, who would die at the end of the film clearing the way for Anakin. This is a rather lame and predictable course of events, so eventually Lucas decided to switch the master and apprentice.
-A quick side note, do you think people watching Star Wars in order with no knowledge of the original trilogy would mark Obi-Wan for death in TPM? Qui-Gon is the main character, Anakin looks to become an important player in future events, Qui-Gon wants to train him, but Obi-Wan being his apprentice forbids this. I think it will be an interesting turn on our thoughts, as we know Qui-Gon must die to make way for Obi-Wan, but those watching the saga chronologically will assume Obi-Wan will die to make way for Anakin.-
Back to the matter at hand, as VS pointed out, Qui-Gon IS a HUGE continuity error. But looking at the origins of his character he could have been nothing else. He essentially replaces Obi-Wan's assumed role in the beginnings of the saga, and really messes things up in the original trilogy. Now Obi-Wan was not the Jedi who discovered Anakin was a great pilot and was amazed how strongly the force was with him, or was willing to take it upon himself to train him as a Jedi, it was Qui-Gon. The bond we all felt develop between Anakin and Qui-Gon really should have developed between him and Obi-Wan. Without it, we are left with a bitter apprentice who had hoped for a better master endlessly bickering with his bitter master who only trained the boy because it was his dying master's last request. You thought Obi-Wan was a liar in ANH, he's an even BIGGER liar in RotJ. No certain points of view can explain THESE inconsistencies.
This also ties into Obi-Wan's age. Lucas has said time and again the ANH lightsaber duel is so dull and slow because Vader is a half-machine cripple and Obi-Wan is an old man. Alright, fair enough about Vader, but Obi-Wan an old man? He's 25 in TPM, 35 in AotC, 38 in RotS, which makes him...56 in ANH. Wow. "Surely he must be dead by now," Tarkin said of Obi-Wan. HE'S LESS THAN SIXTY YEARS OLD!!! Not to mention Qui-Gon was in his prime as a Jedi at 50. Once again, Qui-Gon's existence hurts the saga.
To me at least, it is quite obvious that Obi-Wan should have been around 40 in TPM, and discovered an 18 year old Anakin Skywalker, the best starpilot in the galaxy. Amazed with how strongly the force was with him, Obi-Wan would take it upon himself to train him as a Jedi. Anakin would grow into a cunnning warrior, a powerful Jedi, and most importantly, a good friend. This would make his fall to the darkside and fallout with Obi-Wan all the more tragic. Why Lucas felt the need to do things the way he did is beyond me.