Sentinel Prime is a walking Shout-Out to The Tick, including his blue coloration, giant chin, and occasional lines like "Energon-y goodness". His character was actually designed after actor Townsend Coleman was cast.
Development Gag: Team Athenia (Rodimus Prime, Red Alert, Hot Shot, Brawn, and Ironhide) is three-fifths scrapped ideas (see the first entry under What Could Have Been). Sari's scooter / jetpack is based on a transforming trike she had in a dropped version of the opening sequence.
"Teen Titans", by some Transformers fans (G1 or other media) who believe the series is an inferior incarnation of the whole franchise, Ironically, the show was designed by the same team who worked on the aforementioned series.
Since, in this continuity, Autobots are largely incapable of flying, the Animated version of Powerglide actually seems to transform into a ground-based alternate mode, prompting some to name him as "Powerdrive" instead.
The third season was released by Shout! Factory in June 2014 along with a DVD set of the full series. Unfortunately, the Shout! Factory releases do not include any of the short films and there are no scheduled individual rereleases of the first two seasons.
Sparkplug Witwicky from the Generation 1 cartoon makes some Continuity Cameos in the episodes "Nature Calls", "Sari, No One's Home", and "Three's a Crowd", but his voice actor is never consistent. He is played by Jeff Bennett in his first appearance, David Kaye in his second, and by John Mariano in his third appearance.
Science Marches On: Blackarachnia speaks these exact words to justify her Predacon research.
Also, in a more real-world context; there's the updated forms of the Dinobots. The G1 Dinobots were already somewhat inaccurate even during the 80s, with different body proportions to the animals they were based on. By today's standards they are hideously inaccurate, with their stances and movements being made to reflect the idea that Dinosaurs used to be thought as slow and dumb. The Animated Dinobots are much, much closer in general accuracy to their respective animals in virtually every way. Body proportions, stances, range of movement, everything.
Screwed by the Network: Sure, three seasons and 42 episodes doesn't sound too bad... until you realize that the show was on the air for less than a year and a half.
Short Run in Peru: Somewhat annoyingly to American viewers, Canada's YTV aired this show a week ahead of Cartoon Network after it was dropped for one week in favor of the Ben 10: Alien Force premiere. Not to mention that, annoying everyone else in the world, a Dubai children's network aired almost all of season 2 over a month early, leading to Wild Mass Guessing and outright misinformation based on screenshots with no English translations.
Show Accuracy/Toy Accuracy: For what it's worth, Animated has some of the best accuracy between the show and the toys of any continuity, in that the toys are highly accurate in Alt Mode, Robot Mode, and have extremely accurate transformations, all while maintaining the series' unique art style.
Shrug of God: Derrick Wyatt himself prefers not think about what Slipstream represents. He's also keeping mum about how Sari's protoform ended up in Isaac's lab - he feels that something like that should only be told in future TFA fiction. Fingers crossed...
Talking to Himself: Due in part to budget, Animated gets a lot of mileage out of its actors.
Pushed to its logical end with the Starscream clones. Despite having color schemes clearly inspired by older characters that had their own names, they'll probably never be referred to as anything but Starscream clones on the show. That's because if they're all Starscream clones, then they all count as the same character; if they were different characters, they'd have to pay Tom Kenny extra to voice them all and they're only allowed to have one VA voice so many characters in a single episode.
They've done several episodes where two characters go out on their own and argue the entire way, and often even had the same voice actor, with both Prime/Grimlock and Prowl/Fanzone.
This was lampshaded during the Botcon 2008 script reading, where Bumblebee suggests to a thinly disguised Beast Wars Megatron (as voiced by David Kaye) that they call Grimlock or Lugnut (both voiced by David Kaye) for help. Megatron responds "Oh, please. What do I look like, Scott McNeil?"
There's even one where Animated!Optimus is talking about golf with BW!Megatron, the latter declaring with a chuckle that Autobots suck at golf.
Throw It In: Blitzwing's German accent was a last-minute improvisation by Bumper Robinson while auditioning for the role, no doubt based on the character's name. When he got the part, Blitzwing was hastily redesigned to compliment the accent.
Hot Shot and Red Alert were meant to be part of the main cast, but were replaced by Bumblebee and Ratchet. Rodimus was first choice for the 'jerkass on the Elite Guard' character, but this was apparently nixed by Hasbro.
Also, Hot Shot was going to receive a toy later in the toyline, along with a triple changing Megatron, but both only made it to the prototype stage before the series was nixed for Revenge of the Fallen.
In the episode "Autoboot Camp", originally conspiracy crazed Cliffjumper was to be the Autobot framed for being a Decepticon spy, but Hasbro did not approve of that and that role went to Wasp.
The second Allspark Almanac goes in depth about what Season 4 would have been like - and it sounds like it would have been the best thing in the world, too. No, we aren't going to give the details, get the book yourself. note If you really want to know, we've got three words for you: Shattered Glass Animated.
Derrick Wyatt mentions that they were planning on setting up a fight between the Dinobots and Constructicons in Season 4.
The Animated producers were hoping to get Eric Idle to reprise his role as Wreck-Gar from the movie, but he was too busy with Spamalot, so they ended up getting "Weird Al" Yankovic instead. Though the final Wreck-Gar owes a lot more in appearance and mannerisms to Weird Al than Idle, his debut episode still contains a few ideas that were formed back when they were trying for Eric Idle — most notably his team-up with Angry Archer, whose voice is very clearly an imitation of John Cleese.
Some scenes also had to be cut for time or for other reasons, as revealed in this interview. The most major one? Megatron beating the tar out of the Dinobots.
Another one was that Starscream was apparently supposed to have a fairly quiet voice, as Marty Isenberg really disliked the screechy voice G1 Starscream had. However, after advice from Derrick J. Wyatt and hearing Tom Kenny's performance he decided to compromise with a voice that was high and a bit whiny, but not outright shrill.
Afterburn, the Canon Foreigner from the Titan Comics, was originally going to be named Sideswipe, and preview images even called him that. He was given a different name due to fans hating the design, along with the possibility that Hasbro intervened due to his nature as The Mole, similar to the Cliffjumper example.
The series was originally titled Transformers: Heroes.
Word of God: Several things, most notably the possibility of Blurr not being dead, and Slipstream's name.