Screwed by the Network: A common complaint from fans over cancellation, though Joe Quesada, Arune Singh, and Josh Fine have stated it was simply a financing matter. One of the other companies reportedly folded and no substitute could be found.
This series was originally conceived as a solo Wolverine show.
It had been announced that Deadpool would be appearing in season 2, with Nolan North reprising his role from Hulk Vs.. This led to much rejoicing. And then they canceled season 2. One can only imagine the hilarity of hearing North alternate between Cyclops and Deadpool if given the chance.
According to multiple interviews, Emma Frost would have turned out to be Not Quite Dead and trapped inside of Jean. Obviously this didn't happen and Emma ended up being Killed Off for Real owing to the cancellation.
Associate producer Joshua Fine had reportedly considered incorporating tie-ins with the then-upcoming cartoon The Avengers: Earth's Mightiest Heroes, such as Wolverine teaming up with Hawkeye and Black Widow on a black ops mission. (Incidentally, some tie-ins with this show did make it into The Avengers, such as Nick Fury asking one of his agents to send Whirlwind to the MRD.)
Season 2 production art that leaked on line showed that Cyclops and Jean Grey would have worn slightly modified versions of their 90s Jim Lee era costumes, with Jean getting long hair again while Cyclops's suit would have been sans trunks in favor of just having blue pants under a yellow belt.
The writers have also stated that had season 2 gone forward fans would have finally seen Cyclops rise up and redeem himself and become the hero we all know him to be, but given that this show was one big love letter to Wolverine (to say nothing of the fact that the cliffhanger showed Cyclops would have spent have the season working for the bad guys) this seems highly unlikely.