I'm not sure how to use Plan Omega. I can see the dialogue option when I have Rogue with me and we're in Xavier's office, but when I click it she just says: "Huh?" and it doesn't seem to work. Do I need to talk to her about it first? What's the pre-requisites?
I think she has to be a high enough relationship with you as well. If her stats aren't high enough, then she doesn't 'know' plan omega.
Speaking of which, it seems to be a LOT harder to raise stats now. Neither rogue nor Kitty will give me the time of day, even though Rogue's love is over 600. She won't date me, slaps my hands away if I try and flirt, etc... Same with almost all the other girls. I even resorted to giving a gift to Kitty early, and she still won't let me flirt or even ask her on a date.
Emma, on the other hand, can't keep her hands off me.
Not sure exactly what has changed, but maybe there is a new mechanic I'm not familiar with, like if you don't show a girl enough attention she cools off towards you. Maybe a glitch where she stays mad forever. We weren't a thing, I didn't cheat on her or even get to first base. If that is the case, I have no idea how to warm them back up. At this point I'm just planning on breaking Emma and seeing if she can help me seduce the other girls.
Edit: I eventually gave up and gave Rogue a book gift, which jump started her. She went straight form "don't touch me, you can't come in, no I won't go on a date with you" (at 600+ love) to "you better be my boyfriend", which means no more sexy time with Emma until I break Rogue...