In "Shredder Strikes Back, Part 2," Raph flashes back to the Shredder's (first) defeat, and states that "Nothing human could have survived that!" Much later, it would be revealed that the Shredder isn't human.
In "Exodus," it was promised "One of these characters will never be seen again", and after the episode, Ch'rell is banished to an ice planet, likely never to be seen again... That is, until Turtles Forever, but even before that, Peter Laird confirmed that the Triceraton Shredder shown in concept art of a possible second Fast Forward season would have been Ch'rell hijacking the body of a Triceraton soldier, and Back to the Sewers not-so-subtly implied in its first episode that Ch'rell would fight the other two Shredders in the show (there would have been an arc called "The Shredder Wars"), making the claim that Ch'rell would never be seen again hysterical.
On a similar note, there's this exchange, from Season 5, before the Cyber Shredder was introduced (and, consequentially, before Turtles Forever and the whole 'Multiverse' thing).
Early on in Season 1— the episode "The Garbageman"— Mikey tries out several catchphrases, much to his brothers' distaste. One of those catchphrases is "It's trench-coat wearing time!". Nobody (except the fans) seems to have a problem with "It's ninja time" five seasons later.
The Dark Turtles from the Fast Forward season have far more distinct designs than the Turtles, with Dark Leonardo having the most balanced physique, Dark Raphael having a bulkier form, Dark Donatello being taller and slimmer, and Dark Michelangelo being somewhat smaller than the rest. Barring Michelangelo, almost all of the design traits are exactly like the 2012 incarnation of the Turtles, who were all made distinct aesthetic-wise. Dark Raphael also has spikes protruding from his body and shell, which also makes him resemble Raphael's mutated pet Turtle Spike, who would become the 2012 incarnation of Slash.
"The Return of Nano" has a bit of back and forth on Not a Date between Casey and April. During the climax, Donatello needs April's help for his plan and runs off with her, leading Casey to bemoan "that sneaky, little green nerd" running off with his date. This exchange got funnier in light of the three characters being in a love triangle in the 2012 series.
The 1987 series was a Lighter and Softer show that received a retool late in its run that made the last couple of seasons Darker and Edgier. The same thing happened to this show, but in reverse: This was a Darker and Edgier show that received a retool late in its run that made the last couple of seasons Lighter and Softer. Also, both retools wound up being very unpopular with their respective audiences.
An animated adaptation where a long-running reptilian team is transformed into dragons to tackle a worldwide threat. Are we talking about the "Ninja Tribunal" season or the fourth Sgt. Frog film?
Mikey is a superhero fanboy who becomes a superhero himself (specifically a Badass Normal in a show full of powered hero, meets numerous superheroes (including Nobody, who bears a superficial resemblance to Comic Book/Batman), and becomes a reserve member of the Justice Force. Fast forward to the Nickelodeon era and the TMNT have crossed over with Batman multiple times.
The series ended up having a lot of similarities with the Teen Titans series that came out the same year (of course, Teen Titans is considered to be one of the inspirations for the original comics):
Kluh was introduced in the Battle Nexus storyline as a HULK MASH!-Up character and whose name was a Sdrawkcab Name of "Hulk" in the early 2000s. Many years later, Marvel would actually introduce a villainous Hulk character named "Kluh" who was an intelligent incarnation of Gray Hulk.
