Actor Allusion: In "Human Error", Human!Bulkhead is dressed like an American Football player. Likely a reference to Bill Fagerbakke' role as Dauber, a college football player on Coach.
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.
"Teen Titans", by the TF-fans who belive the series is "Ruined FOREVER" (as usual), since it 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.
They brought back several of the same voice actors who worked on G1 to reprise their characters. Most notably Corey Burton as Shockwave and Spike Witwicky; but also John Moshitta as Blurr, Susan Blu as Arcee and even Judd freaking Nelson for Rodimus Prime's few lines in TransWarped.
More Japanese voice cast, a few of whom are actually TF veterans, such as Roy Mustang as Ratchet and Urataros as Prowl to name two. Renji of Bleach as Lugnut and Fumihiko Tachiki as Prometheus Black/Meltdown as non-TF vets.
Homage: Mainframe is such an homage to the original G1 character that, like the original (an altmodeless Action Master), he never transforms. Word of God is that he does have an altmode, but it's an immobile supercomputer.
Fortunately, the third season is scheduled for release in june of 2014, as is a DVD set of the full series. Sadly, no individual rereleases of the first two seasons are scheduled.
Ninja Pirate Zombie Robot: It's later revealed that Lockdown was once a ninja pupil himself and an Autobot; Word of God is that no Decepticon ever trained under Yoketron. And Oil Slick is a ninja chemist.
The Other Darrin: In season three, Omega Supreme is voiced by Phil LaMarr instead of Kevin Michael Richardson.
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.
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.