Actor Allusion: In the episode "Turtle Temper", Raphael (voiced by Sean Astin) is forced to go home by the other turtles because his temper got the best of him, but came back when his brothers are attacked by Spider Bytez, who was actually the mutated Vic. Does this look familiar?
All-Star Cast: Aside from some legends in the voice acting community (Rob Paulsen in particular makes his return to the Ninja Turtles after twenty years), the show also has legitimate movie stars (Jason Biggs, Sean Astin, Kelly Hu) slumming it to play cartoon turtles. Mae Whitman as April, Greg Cipes as Mikey, and round out the cast with lower key TV and movie Stars.
Corey Feldman (Donatello's VA from the first & third live action films) voices Slash, the mutated form of Raphael's pet turtle Spike. This is actually a twofer, as aside from Feldman's previous work in the franchise, Raphael is voiced by Feldman's former Goonies co-star Sean Astin.
Kevin Michael Richardson previously voiced General Aguilla, the Big Bad of the 2007 TMNT film.
Renae Jacobs, who voiced April in the '87 cartoon, is voicing April's mother, or rather a monster disguised as her mother.
Creator Backlash: Ultimately subverted. The creators mentioned that they began to hate Dogpound, to the point they nearly killed him off in the second season. He was Rescued From Their Scrappy Heap when they had him mutated into a new incarnation of the classic character Rahzar.
Dawson Casting: The youngest Turtle voice actors are Greg Cipes (31) as Michelangelo, followed by Jason Biggs (35) as Leonardo, Sean Astin (42) as Raphael, but the winner is Rob Paulsen voicing Donatello at age 57. Leo's follow-ups Dominic Catrambone and Seth Green (40) also count. Mae Whitman comes closest to her character April's age at 25. note If she was playing a traditional adult-aged April she'd be just right.
People have guessed that Spike, Raphael's pet turtle, due to his name and being a Turtle, would wind up being mutated himself. This thread, featuring concept art from Nick Magazine, confirms that Spike will become Slash.
The revelation that Karai is in fact Miwa, Splinter's biological daughter.
Lying Creator: Before Slash's debut his voice actor claimed that Slash would be an ally to the Turtles, and the perfect companion to Raph, a description that would come to fit better Casey Jones. And then "Newtralized" happened.
Some months before "The Wrath Of Tiger Claw" aired, some scenes from a storyboard were leaked on tumblr where Splinter tells Karai that she is his daughter and later it is seen her confronting Shredder about this. When people asked Ciro Nieli if these scenes were real, he said no. Comes the episode with this same exact scene and now people is left wondering, specially because the other leaked scene was a kiss between April and Donatello that also turned out to be a real scene come the Season 3 episode A Foot Too Big.
At Comic-Con 2013, Ciro Nieli claimed Irma would be Mikey's love interest. Unless there's a real Irma out there, there's no chance of that.
The Other Darrin: Dominic Catrambone voices Leonardo in all Season 2 episodes produced after "The Wrath of Tiger Claw" instead of Jason Biggs (due to his wife's pregnancy), just as he voiced him in the video game. After that, from Season 3 onwards, Seth Green takes over the role, where it is explained in-universe that Leo received throat damage in his fight with Shredder.
Schedule Slip: Release dates of the episodes have a somewhat bad tendency to jump around to another date or be several weeks after the most recent episode. Particularly noticeable with "Parasitica", which had been announced to be a week after "Pulverizer Returns!", but then got delayed to June 1st, and finally aired on July 20th. The episode was, however, aired in other countries, but went through similar problems.
Shown Their Work: There are a few scenes that indicate that the writers have done some research, like the difference between "Venom" and "Poison", and how a Wasp dies when the stinger breaks off, though Artistic License does still factor in (like the latter being a Parasitic Wasp, which are one of the types of Wasps that don't die from their stingers breaking off).
Also, Japanese culture references are, for the most part, surprisingly accurate and tasteful, and are very rarely used exclusively for Rule of Cool. Even if subtle moments, like when Splinter is shown meditating in "Of Rats And Men"; he uses real Shintoist hand gestures (or "mudras").
Type Casting: Rob Paulsenhimself has gone on record saying that if you have to do a TMNT revival, then you also have to have Greg Cipes as Michelangelo. Even before that, Michelangelo holds the same role in the Turtles that Beast Boy (Also played by Cipes) held in the Teen Titans.
Corey Feldman (Donatello's VA in the first & third movies) auditioned for the role of Raphael, which would've added a whole new level of meta-humor to the casting by having Feldman & Paulsen switching Turtles from the last time they worked in the franchise.
Character bios were leaked when the show was still being worked on, and Shredder's stated that he had a daughter named "Oroku Miwa" who allowed him to stay human. The name "Miwa" is used for the name of Splinter's daughter in the show (Splinter's bio still mentions a lost daughter, though suspiciously leaves her unnamed). Shredder is still a pretty terrible boss and human being, and ultimately, the show kept the traditional Karai and Shredder match-up albeit hinting that Karai is actually Splinter's daughter, Miwa.
Some of the first concept art reveals that it was planned for Raphael to be the one to have the crush on April, but later the screenwriters decided that it suited more Donatello.
One piece of rejected concept art showed that there were once plans to have Wingnut and Screwloose appear on the show as Expies of Batman and Robin, but instead Wingnut became nothing more than a nickname for Kirby O'Neil's mutant bat form and Screwloose was never given a mention at all.
The production team actually began to dislike Dogpound so much they seriously considered killing him off in season two, but they declined, instead mutating him into this series' incarnation of Rahzar, who they had wanted in from the beginning.