well, for Batman Beyond, the decided they'd start Terry McGinnis' New 52 storyline by killing him off in the past, and having a slightly older Tim Drake replace him, because that's what the fans like? just the costume? not the guy who had to deal with the death of his dad, teenage issues, and the fact that he was genetically spliced with Bruce Wayne's DNA from back when Terry was still in his dad's pants, right? who cares about that stuff?
and for Superboy, they took a really likable character who dealt with issues such as "am I gonna become Superman or Luthor? I mean I have both of their DNA" and picking up the pieces of friendships that he left behind after he died in Infinite Crisis, and instead made him a weirdo little prick whose only likable factor is that he has a tron suit I guess.
so when I clamor on about Terry McGinnis and Conner Kent being added into the game, it's because I got jipped out of them in their own media homes.