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-Breaking Character: Venus. Most fans see her as a Replacement Scrappy for April O'Neil, 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. It's particularly telling that even the franchise's creators have differing opinions on her: While Peter Laird is well-known for outright despising the character, Kevin Eastman has gone on record to say that he likes the character and hopes for her to someday make a comeback.
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 Plot: In an early episode, Donatello snaps at Venus and Splinter remarks the guys are still having trouble seeing her as part of the group. That was more of an Informed Attribute, as Venus really had little trouble integrating into the group, but it could've been interesting to see her struggle and change up established dynamics in the process.
Villain Decay: Dragon Lord and the Rank. Dragon Lord mostly because in the Five-Episode Pilot he almost kills Splinter and it takes all the turtles the bring him down. A dozen episodes later Dragon Lord is defeated by itching powder while the Turtles humiliate the Rank by dressing them up like babies…