What makes you think anything would be better?
The mutant race becoming endangered wasn't Cyclops or Wolverines fault and they couldn't have prevented it.
The X-men going to war with the Avengers would still have happened. The Phoenix would still have come and Storm was on Cyclops side during that fight.
The mutant race becoming divided wasn't a Scott vs Logan issue it was about whether or not it was necessary for students to be prepared for battle. Once again Storm stayed with Cyclops and even Rogue had a difficult time deciding.
The Black Ops team wouldn't have been formed if Storm was in charge but it probably would have if Psylocke was seeing as she became a member of the second team. Other than being ethically immoral the black ops team was necessary and probably one of the most effective decisions Cyclops/Wolverine has made.
The decisions weren't based on whether the character was male or female but on their personality. Even still most of the decisions were made out of character to further the story. Take schism for example, Wolverine was portrayed as the caring protector of children while Cyclops was portrayed as a man who wouldn't give a damn if they all died. But up until that point Wolverine barely interacted with any of the students while Cyclops mentored a few of them and actually cared about them.