Audience-Alienating Premise: Not the book itself, but the adult-themed continuation, Ninjara: Seed of Destruction. If being published in the franchise's Audience-Alienating Era wasn't enough to do it in, then being published in the Furry Fandom anthology comic Furrlough ensured that even hardcore fans wouldn't look in its direction.
Anvilicious: Certain stories, especially ones written by Mirage staffer Steve Murphy, could be rather heavy handed when it comes to portraying the evils of pollution, deforestation, global warming, nuclear power, and pretty much whatever was bothering him that day. They usually didn't interfere with the story, and there was still plenty of action to balance it out, but at times it could almost reach Author Filibuster levels.
Growing the Beard: There are some debates as to where exactly the comics hit their stride, but at the very least, issue 5 marked the moment the series moved away from being simple adaptations of the cartoon episodes, and began to have its own identity.
Harsher in Hindsight: Ninjara leaving Raphael for Mokoshan is already considered by many to be a Tear Jerker, but at least you had the sense that she was still going with a good man. The official, adult-themed continuation called Ninjara: Seed of Destructionsaw Mokoshan himself get assassinated, essentially leaving Ninjara alone once again. Even worse, the plot point of who killed him never got resolved, essentially meaning Ninjara's story ends with heartbreak.
The comic was easily the darkest book Archie Comics published at the time, which led to several problems with the editorial because of the more adult content. In the 2010s Archie has started publishing severaldarkertitles in order to reach an older audience.
In the chronological series finale of the Archie series, Raphael and Ninjara's relationship came to a close, with her growing closer to the wolf-man Mokoshan and Raphael and Mokoshan eventually coming to blows over Ninjara. Years later, with the 2004 re-launch of Tales of the TMNT, set in the Teenage Mutant Ninja Turtles (Mirage) continuity, Mirage Raph has multiple fights against werewolves and while no werewolf ever steals his girlfriend, the first issue with Raphael battling werewolves involved a werewolf cult luring away a loved one, in this case his human foster-niece Shadow, in order to try to turn her into a lycanthrope. After that encounter, Raph goes on to have a few more adventures battling werewolves in separate adventures and humorously comes around to hating werewolves in general.
It's the Same, Now It Sucks!: How many fans feel about the early issues that adapted episodes of the show; if you've seen the original episodes, you already know what happens in the early issues. This might've been acceptable at the time, but with no shortage of options for seeing the original episodes these days, many will suggest skipping straight to issue 5 if you're not too particular about having every comic.
What Do You Mean, It's for Kids?: Some of the later stories rivaled the original Mirage comics in terms of grittiness, even though this was the kid-friendly TMNT book. This unfortunately led to problems with the editorial staff at Archie Comics that led to the series getting cancelled.
To elaborate: The Mutanimals were brutally shot to death on-panel. Despite time-travel being involved, the team stayed dead. When it was revealed the demon Null was behind it, he disguised himself as one of Candy's deceased friends just to torment her with an image◊ of the Mutanimals burning alive in hell.
Another storyline had future versions of the TMNT travel to the past, where they met up with Adolf Hitler. They tricked him into committing suicide◊.
◊ of the Mutanimals burning alive in hell.
