Honestly, I saw the whole Professor X situation in Season 1 as a bit of a compromise that didn't go well, and that is something Craig Kyle has hinted at in some interviews. He noted in the producation stage they knew they wanted to have to justify why Wolverine was in the position to lead. That meant somehow getting rid of Xavier. He and Johnson didn't want to outright kill Xavier, but they wanted him incapacitated. Unfortunately the "limbo" they have attained, where Xavier only leads them "sometimes" is much like those compromises where no side feels like they got what they wanted. It has kept Wolverine from really leading; all he does is hold the team together until Charles gives orders, which frankly Storm or Beast could have done with sufficient writing. It takes a little away from Logan's feat.
Some of the "Future X" episodes were pretty decent and had some good moments, but it is hard for me to really take Logan as a leader when all he does is act as Ghost Head Xavier's go-between, which nearly any X-Man would do.
Hopefully the writers change this dynamic in Season 2 and do not just repeat it. Xavier as Zordon got a bit old after 26 episodes; after 52 it will seem lazy.