I think people are overplaying Cyclop's treatment in this show. I've seen the last several episodes and they are fairly kind to him, especially considering he isn't the focus. Although it's not apparent, the show does give a reason for his ineffectiveness, and it's his loss. This at least is a sensible explanation. He has lost Jean and now he has become a shell of himself. I've noticed, as far as fights go, he gets pwned a hell of a lot less than Wolverine, in fact he's the most competent on the battle field. If this next season is [blackout]Age of Apocalypse, like it seems to be, I eagerly looked forward to them animated the prelate saga. Showing him as the leader of the pens, exploring his mercy and compassion, and proving that his allegiance to the Xavier dream is more than just a blind following[/blackout]
I think that battle field presence may be more about BS&P than Cyclops' confidence. Think about it. Wolverine is a network TV dilemma. He is popular, exciting, and so forth. But he can't actually use his claws on camera against most enemies that aren't robots or objects because of censorship. So all of Wolverine's fights on most TV shows are hindered by what he can't do with his claws, which is damn near everything that is what we attribute to Logan from the comics.
Cyclops, on the other hand, just zaps people with energy beams. That has been fine in network cartoons since the 60's. So it is easier to storyboard his action sequences, I would imagine. One doesn't have to write or pace them with half a mind to what the network will not allow as they have to do with Wolverine on TV.
Plus, Wolverine is one of the only characters on the cast who can take insane amounts of damage and, due to his powers, can recover from them quickly without being forever crippled. So, much as in Evolution, he is used to showcase how tough a threat is. Cyclops (or most characters) would be dead or hospitalized if a giant monster threw him 200 feet into the sidewalk, but Logan will be peachy in a few minutes. Colossus on a cast would help balance this sort of thing, but the writers don't like him.
Imagine if Batman wasn't allowed to throw Batarangs, punch people, or jump through windows. That is the dilemma Wolverine usually faces on TV. His most well known tools are dulled for outdated BS&P who aren't aware that the same children they wish to shield curse like sailors on any first person shooter X-BOX or computer tournament and/or are exposed to much worse things from pro wrestling, the internet, music videos/songs, and cable movies. Maybe my view on kids is cynical, but to paraphrase someone, cynics are usually right 9 times out of 10. In the 1980's, I thought it was completely ludicrous that the Ninja Turtles couldn't use their bladed weapons on any flesh and blood enemy. I can imagine the children of the modern age find this stuff with Wolverine even more ridiculous. But until the mainstream American method of preparing children for harsh realities shifts from "keeping them ignorant as long as possible yet hoping they learn about sex/violence in a manner that is safe and doesn't inconvenience us in the middle of CSI", this may never change.
Anyway, about Cyclops. The downside of the method that WOLVERINE AND THE X-MEN went into the show is that you have zero context. It assumes you know how these characters are supposed to act and their origins, but as the show picks and chooses what it likes from the mainstream comics, Ultimate, the movies and prior cartoons, that foreknowledge can change at any moment. The moment we see Scott, he is apologizing to Jean for unfairly insulting Logan and making her angry, and it seems very clear that Jean has definite feelings for Wolverine, blowing him a kiss. The moment he loses both her and Xavier, Scott abandons the rest and shows no endearing qualities. He is content to hide away for a year while the world gets worse. He all but forces Logan to take command by violently refusing to. He only suits up again to find Xavier (not even backing up Beast when he claims Logan's method of confronting Magneto is less than ideal), and then immediately afterward needs Future Xavier to practically beg him not to abandon his friends again, like a spoiled child. He would have left Storm to Shadow King's mercy in "Overflow" if Kitty hadn't happened to complain about him too close to his door. From there he is oblivious to Emma Frost's mysterious attraction to him and sees her only as a method to find Jean. Kitty makes a big deal in some episodes about Scott acting "out of character", but the problem with the show's format is that this IS his character.
Bluntly, Cyclops in this show is almost the cliche of what people usually say about him when they justify not being into him. He's a selfish spoiled brat, or, when he isn't speaking, which is most of the time, he is Dull Optic Blast Man. When he doesn't get his way, he mopes and has no will to fight for anything, even his friends, unless someone dangles his girlfriend or his mentor in front of him. The Cyclops that people loved in EVOLUTION, who took charge while also being compassionate to the feelings of others and even being capable of mending fences is not here.
If you believe
TheVileOne's run down of episode 12, Cyclops is even willing to endanger the public and drag the X-Men into fights that aren't their business just to try to get what he wants for himself. Now, I don't completely buy that angle, but it is a valid way to look at it. This isn't an endearing quality. It makes it easy for Logan to seem like an ideal leader in comparison. Wolverine is often written, consistently, as being the core of the X-Men because he will always fight with them and for them, even when he disagrees with something or doesn't really want to, because he believes in the cause despite himself and his past. Logan may snarl and growl about it, but he will never abandon the X-Men; that is why he reorganized them in this show. That's why people rotate to him as fans of the franchise. Cyclops, at least so far in the show, is the exact opposite. The minute he loses what matters to him, the X-Men could all die for all he cared. He abandoned them, and would have continued to do so without constant needling or coddling. That isn't endearing. It may be a "sensible explanation", but it isn't endearing. Audiences have no mercy for mopers who can't suck it up for the greater good, like Logan usually does.
People like the idea of Logan and Scott swapping roles. The problem is that they don't if you get down to it. When Logan is being the rebel who doesn't listen to the leader, makes mistakes, goes on loner quests or makes wisecracks on occasion, he is written as being the coolest thing EVAR, and the situation always works out for him. When Cyclops does the same now, the situations are written to where he needs to be bailed out or he comes off looking like a chump who doesn't take missions seriously if they don't personally involve him. Can you think of any animated episode anywhere that made Logan look like a chump because he didn't listen to the leader? Because I sure can't. Hell, three movies pretty much reinforced the idea that Logan ignoring whatever Cyclops says and fighting battles his way saves the day, every time.
The writers also have a thing for Cyclops completely ignoring women who are flawed but genuinely into him because of his blind devotion to "perfect" Jean, who either here or in Evolution always seems just a tad unreachable. In Evolution, Jean was friends with him so long that she was never even romantically attracted unless other characters were. Here, Jean almost seems like the Little Red Haired Girl in Charlie Brown, idealized and unattainable, perhaps with Scott only because she couldn't handle Logan's manliness. While that's paying homage to the comics, I recall being a bit crushed seeing Scott ignore Rogue in Evo for Jean and I do hope his thing with Frost ends better here.
Still, to give credit, Cyclops is faring a lot better than Storm, who has no character arc or much of a character to her in this show, period. It doesn't really bother me because I'm not a fan of hers, but she usually just gives exposition or throws a thunderbolt when needed. "X-CESSIVE FORCE" (episode 12) pretty much provided some of the best Cyclops fight animation ever. While he is a maligned character in the show, they have a clear arc for him. He won't ever get to show up Wolverine, but he'll have stuff to do.
Plus, as I said, ignoring this show just because of some of the fumbles with Scott would be an error for any X-Men fan in general or animation fan in particular. I rant about the flaws a lot, but that is because the rest is good and thus I am aware that the writers are more than capable of producing damn good quality. It isn't like THE BATMAN where most of the time you just shrug your shoulders at the hack writing. I can't wait for the finale for this season. It looks to be big.