From the sound of things, we're looking at a Jean Grey on a proactive mission. She is usually not positioned that way in the comics, so this could get really interesting, depending on how involved she is in the story.
No. Before maddie and phoenix it was one sided. It was only Logan. Jean was just nice to him. She even said that before her merge with phoenix. Even during phoenix saga it was only Logan who was obsessed with jean while jean didn’t care. E.g there is a scene when part of xmen ended up in savage land and he looks at the pic of jean (the one he stole) and talks he had plans for her and him.
When jean was brought back against Claremont’s wish we got classic xmen from Claremont. That was a moment when Jean’s feelings toward Logan were retconed.
What everyone is trying to tell you is that we don't care. Jean being playable in this game at all is a huge surprise; we're excited about that. If your personal whims for the character are so strong they dictate your enjoyment of even AU stories, maybe you could write fanfiction instead instead of nitpicking something you have absolutely no control over.
Now I'm getting greedy, thinking about that possibility of expanding this to include more characters for an X-Men game. Sony has a contract for two more X-games after this Wolvie one, so a team game is not completely out of the real of possibility.
In addition to Logan and Jean, playable Bobby and Ro would be ELITE.