Slash, as a villain. In "Slash and Destroy", Slash is without a doubt a villain. In "Metalhead Rewired", he had a very brief (albeit awesome) team up with the Turtles and other mutants against the Kraang. In "Newtralized", Slash is still an enemy of the Turtles, but he shows there are some lines he will not cross like blowing a building when there could be people in the vicinity of the explosion. At the end of the episode, he fights against both the Kraang and the Newtralizer and his grudge against the Turtles disappears when Raph saves him from being crushed by the Kraang walker. What's really jarring is the fact that Slash appears alongside the other villains in the third version of the theme song. He ends up becoming the leader of the Mighty Mutanimals and his character does a complete 180 on his evil traits.
April qualifies for this trope. She gets trained as a kunoichi, is now confirmed to be half-Kraang and half-human, is immune to Mutagen, and has empathy/telepathy powers. Although this makes her cliché to some, the writers could have actually done something with it. Instead, everything is completely tossed over. Despite her training, she's kidnapped or placed in danger in almost every episode. The half-Kraang, half-human idea is hardly ever mentioned again. Her immunity is understandable, but her powers make her the source of last-minute solutions to problem. As of the love triangle between her, Casey, and Donnie, she's little more than a plot device that is only there to be kidnapped and ignore Donnie's affections. This is somewhat fixed by the "City at War" arc, where she graduates to full kunoichi and eventually fights Shredder to save Karai. Plus, she gets an episode as the central character.
Irma makes her first appearance since the 1987 series to the delight of the fans. There is teasing over when she will finally meet the Turtles and how her interactions with them and Splinter will be like and "A Chinatown Ghost Story" establishes that she may have an unknown, hidden power, which would have made this Irma more fleshed out than the boy-crazy best friend from the 1987 series. Instead, Irma was never real to begin with and was actually a Kraang all along, used solely to find the Turtles' lair and quickly disposed of by Splinter, which rather feels like the writers just gave the middle finger to long-time fans who wanted Irma to be among the supporting cast.
It gets even worse in season three, where Kraang Sub-Prime returns, still wearing the Irma mech suit for no apparent reason, not to mention the Kraang having created an army of robot Irmas to fight the Turtles and their allies. Meaning that we see the good guys wailing on and destroying lots of Irma bots and the last shot we see of one is Kraang Sub-Prime's decapitated Irma mech suit's head floating around with a goofy look on its face, basically making it a "Let's Destroy Irma" festival. By now, it doesn't feel like a middle finger so much as the creators of this show seeming having a hatred for the character of Irma and rubbing it in the faces of the long-time fans that this is all they get.
Xever has interesting chemistry with Raphael, a unique fighting style among all the ninjitsu-using characters in the series, and is a surprisingly threatening and dangerous planner, which makes the second season's treatment (appearing less often and being played more for humor) of the character disappointing. While Season 3 corrects it a bit, he's still not as prominent as he was in Season 1 and eclipsed in screen time by Bebop and Rocksteady. In Season 5, when he goes through a Heel–Face Turn, he never reverts back into human form.
Mikey, in the eyes of some, due to the show implying that some of his less than intelligent actions being due to feeling inadequate compared to his brothers. He NEVER gets character development from this, nor is it explored at all.
Mondo Gecko, to some extent. After his debut episode, there could've been another episode that focused solely on his relationship with Mikey and/or Casey, and the two characters could've easily bonded and went through further development (something which, as stated above, Mikey has been severely lacking). If anything, Mikey and/or Casey could've taught Mondo to defend himself instead of being the Non-Action Guy. Instead, he's cast aside and serves little purpose besides being the Butt-Monkey within the Mighty Mutanimals.
The Newtralizer, despite being in the opening titles for season two onward, only appears in two episodes. Not only is he an assassin and an Evil Counterpart to Leatherhead, but he also has a personal vendetta against the Kraang—again, like Leatherhead—and was out to destroy as many of them as possible. He could've become a backstabbingEnemy Mine for the Turtles and used them to destroy the Kraang, or at the very least could've been a recurring antagonist in season four (especially since it's revealed there are other Salamandarians). Instead, he appears in one episode in seasons one and two. When he finally does show up again in season five? He only appears in a two-episode arc and is quickly killed off by the end of it.
The Rat King/Dr. Victor Falco qualifies as this due to the fact that he's the most personal enemy of the Turtles and a major threat outside of the Shredder and the Kraang, putting out a lot of interesting story ideas (including possible encounters with his former partner Dr. Rockwell and setting up a battle between the monkey and the Rat King). He only ever appears three times, fell to his death in the third, and then his corpse shows up in a fourth appearance in season four, leaving it unlikely he's ever going to return. He also never runs into Rockwell as the Rat King and his relationship with him is thrown out the window from his mutation into the Rat King on, with Splinter taking Rockwell's place as his torture target.
The Neutrinos in the 1987 series were fun-loving alien teenagers and one of them, Kala, had an interesting romantic friendship with Michelangelo. In this adaptation, however, the Neutrinos are simply generic Monster of the Week villains with almost no real characterization and zero similarities towards their counterparts from the 1987 series.
Hattori Tatsu quickly established himself as a new, competent, very strong villain for both Karai and the Turtles, despite being blind. The show seemed like it was setting up Tatsu to replace Shredder and be an Arc Villain for Karai or a Disc-One Final Boss in general. Instead, he gets killed by Kavaxas in the same episode as his debut, thus eliminating any chance of him returning in season five.
Sir Malachi only appeared in one episode and he could have made a profound ally for the Ninja Turtles, perhaps as the Squishy Wizard for the Mighty Mutanimals.
