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?
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.
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.
Sean Astin's The Goonies co-star Corey Feldman has been confirmed for a role in future episodes.
Greg Cipes & Scott Menville previously worked together on Teen Titans.
Jossed: Quite a few people expected The Pulverizer/Timothy to become "The Newtralizer", a toy of a mutant frog of some sort◊ that was shown, and his appearance and name definitely seem to fit the Pulverizer's naming conventions. Come "The Pulverizer Returns", he instead becomes Mutagen Man.
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. Let's just say that, as of Slash's debut episode, these are not true.
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).
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.