Think about this Episode 1 starts when Vader is only a kid. There is plenty of time for Yoda to instruct Obi-Wan. He never said Yoda didn't teach him after he was Jedi Knight.
As for contridictions I don't see any. EU makes hints that the Emperor began to gain power ligitamitly and so far he has. Even the mention of the Sith as only two is a reference to EU and a good one. Exar Kun was betrayed by his legions so future Sith lords only have one disiciple that they can fully control.
Even the prohacy doesn't change things really. Anakin will bring balance to the force, but Lucas doesn't say how. You can use reason to determine that he does it through Luke.
True the "I am your Father" isn't as powerful but it is still powerful.
If anything Lucasarts ignores EU. X-wing you fly around as a pilot who suddenly becomes Luke Skywarlker, Rebel assult basically the same thing. XWA, has Ace turning into Lando. Force Commander gives an imperial command of the Endor mission. I can go on and on.
Give Lucas Credit, it is his vision and me must trust him. anyways what are we going to do about it.