Designated Hero: Karai is a criminal and a murderer who has hurt and killed many people, both innocent and evil. However, the comic presents her as the "reasonable" member of the Foot Clan and she is rarely ever called out for her actions.
Ensemble Darkhorse: Through the reveal of their backstories and their character development throughout the comic, both Alopex and Old Hob have become this.
And then there are Bebop and Rocksteady. Fans are delighted to have them in the comic, and even more so when they are revealed to be incredibly dangerous while still keeping loyal to their dumber-than-a-sack-of-hammers characterization.
The Mutanimals in general are this, thanks to their constant badass moments, variety of personalities and how, much like the turtles, they have become a true family all their own.
Also Don/Alopex, particularly for those that feel that Raph has enough female mutant/anthro love interests (Mona Lisa, Ninjara, Mezcaal) and that the other turtles deserves a chance with a female mutant/anthro love interest as well.
Jerkass Woobie: There is no doubt that Old Hob is a complete jerk with violent tendencies and one very deep-seated grudge, but after seeing his backstory, it's really hard not to feel sorry for him.
Alopex applies for this as well, since it's revealed that Shredder wiped out her old pack so that she'd be left with nothing but the Foot Clan. She's only remained loyal for so long because she's been looking for a chance to kill him.
Moral Event Horizon: Dumber-than-a-sack-of-hammers they may be, Bebop and Rocksteady hit this when they nearly killed Donatello, Bebop holding down the turtle while Rocksteady smashed his back with a sledgehammer.
Nightmare Fuel: In #23 there's the sheer amount of mental torture Leonardo is put through before he winds up joining forces with the Shredder, including seeing a vision of Splinter murdering his brothers, then raising them as killer zombies.
Unintentionally Sympathetic: The scorpion mutant Zodi has some of this going for her. She's not portrayed as a mono-maniacally evil villain as she does team up with the Turtles and her goal is to survive against human soldiers trying to kill her. However, the Turtles are still portrayed by the story narrative as being in the moral right for the most part, being unwilling to seriously maim or kill any of Bishop's commandos, and Zodi is eventually made to listen to them during their teamup. Her ruthless approach to fighting becomes much more understandable considering the Turtles walked into the room where she had taken down several of Bishop's troops and tried to attack her, despite not fully understanding the situation and in fact, it's because Raphael went after her and began to second guess himself after mistakenly thinking he maimed a human soldier that he suffered a brutal beatdown at the hands of Bishop's commandos.
Later on, Zodi mockingly criticizes them for their approach and Raphael punches her, initiating a fight with her despite Zodi not being wrong at all about how Raphael had almost gotten himself and his brothers killed or captured for their hot-headedness. Considering how the Turtles had taken some heavy damage from Bishop's commandos due to holding back and second-guessing themselves in battle over their moral code and Zodi being much more efficient at fighting the human soldiers due to her no-holds-barred approach, Zodi ends up being more sympathetic of a character than originally intended despite not being as morally upright as the Turtles and had the Turtles actually listened to her and seriously considered her point of view, there's a strong chance that Zodi could have actually helped the Turtles fight through Bishop's commandos much more efficiently without having to take the kind of unnecessary punishment that they did.