Megas XLR - A show that had great potential to be one of the funniest action comedy shows that CN could have had, i remember that George and Jody had plans for a feature and also in the third season they will show the origins of the Glorft and the war.
The Secret Saturdays - Another one that could have turn into one of the most popular shows today, it had great characters and story arcs that where just entertaining, not to mention having one of the coolest plot twist on a show and showing that death can be apply on a kids cartoon.
Spectacular Spider-Man - I think one of the best Spidey cartoons i have seen, first to Spider-Man TAS. The show had some nice plot twist and revelations, showing that they can confuse the viewer on the identity of the villain(Green Goblin), i so wanted to see what happened next to the characters like the relation of Harry, Gwen and Peter and see if Mary Jane will finally fall in love with Peter and of course the appearance of the Scorpion and the Hobgoblin.
He-Man and The Masters of the Universe 2003- It was one of those shows that could have done well along with TMNT, the story arc was getting interesting with the appearance of Hordak and his minions, Teela's past, She-Ra and many revelations.
Transformers Animated - One of the few show that was getting interesting in the second and third season. I still hate they put human villains into the show but it was nice to see more of the Decepticons fighting with the Autobots, another season would have work and see a more devastating fight between Optimus and Megatron.