It's just poor writing if Cyclops is portrayed as a moron, tho. It's kinda like writing Batman as a moron.
He was never leader in the X-Men because he was the most powerful. Even by the time Havok and Polaris were introduced, certainly by the time of Storm, Colossus, Banshee and on, he has tended to be overshadowed in that department. He's supposed to have led team after team of X-Men not because he's more powerful than them, but because he's a great leader and strategist. If you write him as just being bone-headed, you don't get the character.