After the X-Men film was released in 2000, Rogue's Ms. Marvel powers have been shelved in favor of presenting a streamlined character.
This makes sense, as trying to explain that this new mutant has already fought a superhero named Ms. Marvel, who is also an Avenger, who also has powers from an alien species (the Kree) would provide way too much story to cover in one movie, especially considering that nearly every character in the X-Men movies have equally complex backstories. Rogue's origin was simplified and her natural power (not being able to touch anyone and absorbing powers) is simple and ripe with story/drama potential.
As the X-Men film introduced a whole new generation to her, probably giving her even more exposure than the early '90s cartoon, it made sense to present her this way in X-Men: Evolution (2000). If Rogue had shown up with super strength and flight, she would have been drastically different than the public saw her the summer before in a blockbuster movie.
Meanwhile in the comics, the powers Rogue absorbed from Ms. Marvel were stripped away. Her powers were mutated in the comics by an alien (X-Men #107, December 2000), which eventually led her to having every power she had ever absorbed, to then having no powers at all, to finally only having her natural born absorption powers. She currently only has her natural powers.
Rogue was depicted without Ms. Marvel's powers in both X2 (2003) and X-Men: The Last Stand (2006), further solidifying the version without Ms. Marvel's powers in the public consciousness.
When Wolverine and the X-Men started in early 2009, it aimed to be more in line with the comics than the films. Even though the series was going to be further removed from the film series that had always shown Rogue without Ms. Marvel's powers, at that point it would be weird and confusing to give Rogue powers that she hadn't had in the comics for almost a decade.