Executive Meddling: Mona Lisa was originally going to be a female turtle, but Eastman and Laird rejected it, so she was reimagined into some kind of lizard, which is why her head and feet look like the TMNT's. Supposedly they still didn't like her even after these changes, and ordered the makers of the show not to use her again.
Network meddling was also responsible for Shredder and Krang being Put on a Bus and replaced by Dregg during the ninth season. They also forced the show's creators to introduce a "hip" new character, eventually resulting in Carter, who was pretty much a Composite Character of not only Casey Jones and Donatello, but also Keno from the second TMNT movie. After these changes weren't liked by the fans, rather than admit they might have been slightly misguided in these demands, the executives fired head writer David Wise and replaced him with a guy who had never even watched the series, speeding TMNT '87 to its demise.
Say what you will about Dregg replacing Shredder and Krang in seasons 9 & 10, you gotta admit having him voiced by Tony Jay makes him a Bad Ass.
What Could Have Been/Missing Episode: There was orginally going to be an episode called "Shredder in Love", but it never got past the script stage. Renae Jacobs even recorded lines for it. Little is known about the plot, but rumours state that the love potions from "Green with Jealousy" might have been reused.