These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Anvilicious: A couple of episodes offhandedly talked about the dangers of drugs and protecting endangered animals(especially turtles).
Author's Saving Throw: Later on in the series in the episode "Enemy of my Enemy" Shredder makes a comeback and later on in the episode its implied he will become a major villain again with the golden shuriken. This episode was most likely made as an apology for how Shredder suffered Villain Decay early in the series. (Granted he doesn't actually come back but still.)
Base Breaker: Venus. Most fans see her as a Replacement Scrappy for April O'Neil as well as a shoehorned Mary Sue, but some fans think that she is an interesting concept and would like to see her return in one of the current Nickelodeon-helmed adaptations.
Hilarious in Hindsight: In "Unchain My Heart, Part 2," Raphael remarks that vampires are a human problem, saying vampires don't bite turtles. Several years later, a storyline in Mirage's fourth volume (written by Laird himself, ironically enough) saw Raph bitten by vampire-like creatures and adversely affected.
The crossover with Power Rangers as the show was aired on FOX Kids when it started. 15 years later, both series would once again end up on the same network. This time on Nickelodeon.
Ho Yay: Leo and Raph still bicker and fight like they used to. Only now they aren't related because someone thought it would be a good idea for possible romance with Venus... Ooops.
They Wasted a Perfectly Good Character: Venus, in a way. The idea of a female turtle is an interesting concept and, if done right, she could've been a decent character on her own and possibly a Canon Immigrant. Instead, she was written a Canon Sue as mentioned above as well as reaching Black Hole Sue-levels to the point where one episode (Ironically-titled "Who Needs Her") outright stated that the Turtles needed her more than she needed them. Not to mention that the reason why the four turtles were Not Blood Siblings in this series was for the sake of a possible romance with her. Basically Positive Discrimination gone horribly wrong.
Another aspect is her focus on the more mystical aspects of ninjutsu could have balanced her with the other four (as each turtle has their own fighting style and weapon) if done well, but instead make her a Canon Sue due to being overpowered.