If Red Hood makes it in it'd be a really smart move for story. Batman is against Superman. Superman needs someone who can handle Batman that would side with him. Jason Todd was Robin and left Batman's crew because he wanted to deal with criminals permanently...and now Superman wants to do the same. Superman recruiting Red Hood would be perfect for story telling. If he's in I'll be hyped because I'm a fan and I won't knock them for adding another Batman character since he would be crucial for story in making Superman vs Batman more strategic and impressive.
No, it would be a waste a slot for a couple of reasons. First, the idea of Batman's protege being on the opposing side of his mentor has been done before and that character is already in game. (Dick Grayson was on Superman's side in the Kingdom Come story.) The story may not be like Kingdom Come, but the point is there is someone already in the game that could and
has fill that role you proposed for Red Hood. And Nightwing being under Batman in the character select screen means nothing; MK character select in the show build was completely different from the retail version. Character placement may not even mean anything since there could be more than two factions in the story.
Secondly, Red Hood and Deathstroke's paraphernalia are too similar and Deathstoke has more going for him. He was in MKvsDC, main antagonist of a popular series, and was teased alongside Nightwing, Aquaman and Green Arrow in the cam shot Boon uploaded in July.