I really do think in Mourinho's head, regardless of his placatory interviews, he's dropped Rooney from the starting XI. Despite two accidental assists, none of Rooney's appearances off the bench have actually improved the team's play. He's made the decision, and so far it's been justified.
In Ibra's case, it's clearly not merited to actually drop him, but I would rest him for this game. Get Martial up front, give Miki his start, get Mata and/or Lingard involved at some point, and Ibra can be fresh for Chelsea, which is likely to be exactly the sort of game we'll need his experience in.