Oh my God, I wish people would stop blaming Bruce Timm for the Bruce/Barbara stuff.
1.) The initial idea on Batman Beyond came from Alan Burnett, who felt it might be interesting if Barbara had an infatuation with Bruce and decided to stay in Gotham. She hints at a relationship, but Terry never hears Bruce's side of that story, so it could be something that Barbara embellished.
2.) It's progression in Batman: Mystery of the Batwoman (DTV), clearly shows Bruce is uncomfortable around Barbara when she is flirting with him, signifying that he doesn't know how to let her down gently. Bruce Timm had NO involvement with this movie. It was produced by... you guessed it... Alan Burnett.
3.) The recent Batman Beyond comics by DC are not canon to the show, so ignore that whole pregnancy nonsense. Just terrible.
4.) Yes, Bruce Timm did produce Batman: The Killing Joke, but it seems the sex scene was something he simply went along with. Something that was developed in the writer's room with Brian Azzarello (poor choice) and, yep... Alan Burnett (Co-Producer).
While Bruce Timm gets the majority of the credit for the DCAU, he was not a dictator on the shows and others had ideas too. Not every idea is gold, but if fans would stop blindlly praising or blindly bashing one person, that would be great. Sorry, BatLobster, I'm seeing this everywhere and it's just old hat at this point.