I think the new Star Wars canon authors are happily ignoring Mr. Lucas's foray back into the universe. A lot of the EU stuff I see is based on the OT and characters developed before the PT. LucasArts seems to focus on the era immediately after TotJ (they even nicked the name Knights of the Old Republic), the Galactic Civil War, and the era after the War (they even nicked the name Jedi Academy). The book publishers commissioned a number of authors to write the New Jedi Order, which was post-OT, and now they're moving into the era after that. The most-hyped prequel-era book is about Darth Vader, still firmly an OT character. Dark Horse has their Republic monthly, but also an OT-era monthly. Their most innovative work has been in the post-OT era (Dark Empire, etc) and the the era between the Sith War and the Battle of Ruusan, inclusive. Now they're going even further into the future, with Cade Skywalker (glad to see they're sticking with, um, "Scotch-Irish" sounding names for the Skywalker family).

In short, most of the Star Wars material being produced now or in the near future is substantially untouched by the Prequel Trilogy, and thus, by Lucas's direct, creative involvement. Lucas did not destroy Star Wars; most of Star Wars is ignoring him by this point. That's what happens when you spin your personal, artistic vision into a multibillion dollar industry and let other people effectively take over for fifteen years.