Warner Bros. Montreal has explained why Batman not being in Gotham Knights is a good thing, as he would "take all the air out of the room".
Although much of Gotham Knights' plot remains a mystery, the main conceit of it all is that Batman has died and left Gotham to the rest of the Bat-family. Warner Bros. Montreal has gone on record several times to say that Bruce Wayne has really died and isn't just being hidden until the end of the game, and has now explained why it thinks it was a good decision to focus the story on some other characters for a change.
In an interview with GamesRadar, a few members of Warner Bros. Montreal explain why Batman being absent from Gotham Knights is actually a good thing, explaining that Batman takes up all of the space in the stories that he's in, and that his being gone gives the characters a uniting purpose and drive.
Executive producer Fleur Marty said, "It simply wouldn't have made it easier to have Batman present at all, actually, because anywhere he is, he just takes up all of the space, he takes all of the air out of the room. And so it was so much more interesting to start afresh without him."
Lead writer Ceri Young went a little further into what this means for the characters, saying, "I think (Batman's absence) really drives these characters. There are various points where each finds themselves asking: 'If Batman were here, I think this is how he'd handle it'. But they don't have him, and so they have to figure out how to do it their own way and that's where a lot of their interest and drive lies."
Although many still don't believe that Batman isn't going to make some sort of appearance in Gotham Knights (come on, it's a Court of Owls story), Warner Bros. Montreal is at least adamant that it's the best thing for the stories and characters.