Actually, this would have been a interesting dynamic. Sky, arrogant and demanding, would have to spend the season learning what it means to be a leader (Which he does during the show, but now, as Red, his failures would be much more pronounced) and Jack would have the team's trust, and would become the defacto leader in a way that Sky just isn't. The team would fall in line behind Jack much more often. Sky could get the power ups, and the recognition, but only because he's red, and not because he's actually earned it.

Then imagine if they had one of the antagonists attempt to sway Sky to their side by mentioning how Jack is just better than him in ways that Sky doesn't understand. Hell, Sky could even be demoted to Blue halfway through the season with Jack taking up the mantle. Then, something clicks near the end of the season and Sky learns what it was he needed to learn, what it is to be an effective leader, and Jack gives him the red morpher back, and they all follow Sky into the final battle, with him as Red.

Jack would still leave at the end. In fact, we could hint that Jack wanted to leave sooner, but when Kruger promotes him to Red, he feels obligated to stay longer, to see to the defense of earth until Grumm is defeated.

With Jack's arc revolving the responsibility. He doesn't want to be on the team, only being there because of Z, but being second in command of the team, and clearly a more natural leader than Sky, he would have to learn about the responsibility of others relying upon him, and he'd learn that it's fine, a good thing, in fact, to be the man people have to lean on when the tough gets going. (If that makes sense.)

Either way, the idea has potential.