ACtually, I beleive they have made the EU stories canon to a certain extent. It boils down to that the movies are the most canon and override everything else. The books, games, comics, etc. are the next level canon. In the case of games where there are options for being light side or dark side (like KOTOR and the JK series) the light side option is considered canon.This would explained in one of those "ask the Jedi Coucil" things on starwars.com. The link for those seems to be broken right now.
Also, Lucas has stated that the EU is a parallel universe that does not affect his films. Thus, he can do whatever he wants with them.
I agree completely about the potential of the Old Republic era in regards to stories. There is just so much freedom there, especially before the rule of two comes about and there are armies of Sith.I also agree about the post-ROTJ stories. While there are some good ones, most concepts seem pretty forced. The story of the Empire and Luke and the gang really is wrapped up at the end of ROTJ and their character archs are complete. In regards to the NJO, the fact that they felt they had to deviate so dramatically form anything Star Wars screams to me that the potential of that era has long since been used up. The other problem is that since all those stories were written before ROTS, there are plot holes and inconsistencies as well as just parts that probably would have been done differently now.