Because Batman's the Batman dude. Most of the major-league villains dislike his presence because he has a rep of dealing with major-league heroes better than they could. That's Batman's uniquity in the DCU--That goes the same for his rogues gallery. No matter how powerful those superhumans (or aliens) are, bats shows that we still have enough power ourselves to eclipse them. That's the whole Batman claim to fame--And it's well deserved.
I'd reboot the Batverse from the end of NML. Cuz', like I always say, that was the best that the Bat-books ever got (not counting individual issues):
After the quake, Batman decides never to return to the Justice League.
Joker finishes Oracle off.
Huntress dies.
Tim and Stephanie either leave or die.
Cassandra becomes Batman's more frequent partner (only when he really needs her) and there's a lot more issues covering him teaching her stuff. So she doesn't learn to talk simply through some psychic deus ex machina.
Batman's relationship with Superman, and pretty much all other superheroes, gets more and more unsteady with every interaction they make.
I actually kind of liked the concept behind War Games, but the story was just awful. I wouldn't mind seeing the idea played out again, but only with a major overhaul.
All I can think of for now.