I prefer Batman TAS to TNBA, but I really enjoy them both. That being said, the one thing I didn't like about The New Batman Adventures was what Bruce Timm and company did with the Dick Grayson character. They had him and Batman at odds most of the time, and showed that Dick actually punched Bruce in the face and left Gotham for a few years. Eventually the character was just dropped without any goodbye story. It was eventually explained in one line in ROTJ that he moved to another city, but we never saw or heard from Grayson in the DCAU.
One explanation that I've heard concerning this treatment of the character was that Bruce Timm himself hated Dick Grayson and originally wanted to use Tim Drake for TAS, but they went for Grayson because the general public was more familiar with that version of Robin. Does anyone know if that's true? And I wish they would bring back the DCAU, if for no other reason to tie up Dick Grayson's storyline. Maybe they could have a post Return of the Joker flashback animated movie where Batman quits the Justice League, takes Dick's and Barbara's respective costumes from them, and forbids Tim from ever donning the Robin costume again. Essentially, Bruce would be on his own, aided only by Alfred.
Actually one of the reason that we never hear from Dick again was the stupid Bat embargo that hit the later series of the DCAU. I suspect that Nightwing would have been a member of the JLU if not for the embargo. After all the artists on the series managed to skirt the embargo slightly by showing Nightwing from behind in an episode of JLU that took place in Bludhaven.