For Totally Spies, I would have made Geraldine Husk as a member of L.A.M.O.S. organization instead of Myrna Beesbottom or Helga. A teaming of Geraldine with Tim Scam and Terrence would have been more awesome.
For The Mummy: The Animated Series, I would do a third season that would incorporate elements from its spinoff film The Scorpion King with Mathayus' reincarnated descendant teaming up with the O'Connell family.
The original TMNT series: instead of the "red sky" seasons, I would (loosely) adapt the "City at War" story from the comics. That way, Karai could actually in this show's universe (she only appears in the Tournament Fighters games). Also, it would be a movie; not one of the live-action movies, but an animated movie based directly on the tv show, with the story set after the end of the 7th season.