Let me make two things clear. One, I am not a fan of the character. Two, I am not referring to everyone here but to the characters in the show itself.
Firstly, Professor X returns from the future and rather than talk to Scott, his prized student and the closest thing he has to an actual son, he gives all the screen time for Wolverine.
Charles: Logan...the world is at stake, which is why I'm leaving my X-men in the hands of an amnesiac, unstable, unpredictable psycho-slasher who could abandon them and run off at a moment's notice...Oh, and hi Scott.
Later on, during the episode where Scott tells Xavier about his theory that Jean caused the explosion:
Scott: Professor, what do we do about Jea----
Charles: Not now, Scott. Mommy and Daddy are talking *Mind-wipes him*
I have always been iffy about Cyclops but, to me atleast, they kind of went all the way in bashing him in the series. Even the other characters comment on how useless he is and no one even looks to him for guidance and advice. In fact, notice he is usually seated in the very last row in the Blackbird. Which begs the question...I know that he and Emma hook up in the comics, but I saw nothing here that would make her attracted to him. They never even gave him an episode to develop their relationship or mature him into someone she could like. And the only solo episodes he got only further served to illustrate how useless he is by getting ignored and/or captured.