I do agree that at best, the Xavier/Scott dynamic was not consistent. The "father/son" dynamic went instead to Logan; Xavier even calls him "son" at one point. I am always bemused by the fact that if Wolverine is such a terrific character, and he can be, why he is always outright stealing character dynamics from other X-Men in some comics or cartoons. I suppose the intention was to offer a "change", but the problem of the set up of the show is we saw so little of the "normal" X-Men that when they are immediately broken down, we don't know from what. The producers claim they were working from an idealized X-Men "you all know", but that is a cop-out. This show, like all comic cartoons, picks and chooses the best continuity and storyline bits from mainstream 616, the movies, prior cartoons and even Ultimate X-Men to weave together it's own bible. You cannot assume "it was just like it was in the comics". The idea was noble; they didn't want to "bore" people with too many episodes of set up since, they assumed after two cartoons and three films, the audience is aware of the premise and the main archetypes. The problem is building anything without a foundation may be faster, but it isn't as stable. I sensed that struggle throughout season one; that tug of war between characterization and plot/action oriented storyline with a check-list of what had to happen and who had to show up. More often than not in Season One, the latter won out. It isn't unusual for such struggles to occur in any 20 minute episode show or a debut season, but it is something I hope has been worked out for Season Two. I imagine no end of scripts had to be cut for time; many episodes were packed to the gills.
From what the show showed us, in the beginning Scott was Xavier's pet student, the one he seemed to reach out to and encourage the most...because Xavier had to; Scott was inept and introverted. However as the show goes on we see that Xavier has started to reach out more to Logan. Some saw it as simple necessity; Logan was the one willing to pull the team together, not Cyclops, and there was a whole time-line to save. Ideally the proper leadership back-up for Cyclops was usually Storm, but she doesn't sell as many action figures. There were moments where Future Xavier was quite cold towards Cyclops; when he, gasp, balked at Xavier seeing no option to deal with Phoenix rather than kill her in cold blood, Xavier shut him out of a psychic communication so abruptly that even Logan was caught off guard by it.
Therefore, my impression was that Xavier was disgusted with Scott in this show, seeing him as a pet student he once invested years of attention to who never met his potential when it mattered. Or even when it didn't. When Logan started to reach that pillar of being an X-Man with far less coddling in a far worse situation, it was natural for Xavier to then gravitate toward him.