Although he had Armodrillo since the last series, Armodrillo is shown to spin his claws like a drill in Omniverse. Giga Drill Break anyone?
In "The Frogs of War: Part 2" we meet Ben's new form "Bullfrag", who is wearing some very familiar looking sunglasses (not to mention Yuri Lowenthal's character's association with a frog).
In "Ben Again", Ben admits to Paradox the idea of a Time War is awesome. Maybe minor and another thing that makes Professor Paradox a Doctor WhoExpy, but Ben's reaction might have to do with his teenage self's voice actor is admitting to being a "Whovian".
In "Showdown Part 1", Ben gives a vague explanation that he used to like Feedback so much because he felt like he was part of him. Teenage Ben and Feedback are both voiced by the same actor.
Malware is a malevolent, computer-based villain whose goals essentially amount to world domination, much like Brainiac, Superman's most well-known arch-nemesis and one of Corey Burton's most well-known roles.
In "Showdown Part 2", after being absorbed into Malware, Ben has a flashback to the past when his younger self was moping about losing Feedback. At the end of the flashback, his younger self confronts him and present Ben forgives himself for losing Feedback, thus regaining Feedback in reality and escaping Malware. This is rather similar to his voice actor's role as Yosuke Hanamura facing his shadow and gaining his Persona.
The sweater Darkstar wears as Dante is similar to one worn by Wesley Crusher.
Adored by the Network: An odd example, since Boomerang, Cartoon Network's vault channel, has slotted it in an early-evening daily slot, with extra slots on weekends. CN proper seems a bit less interested.
Ascended Fanon: It was a common idea amongst fans that Dr. Animo's middle name was "James". Come "It Was Them", Rook refers to him as "Aloysius James Animo".
Development Gag: Swampfire's new form bears resemblance to some of his original concept art.
Executive Meddling: Derrick Wyatt says that the tone being closer to that of the first series was an executive mandate due to the fact that, globally, the first series apparently does the best ratings-wise.
Gwen and Kevin's "college" redesign was the only redesign they were going to get, but executives wanted them to look more similar to their Alien Force / Ultimate Alien designs for their first appearance, so they received "transition" designs for the first episode.
Derrick designed Vilgax with his respirator from the first series, but executives discarded it because they wanted the character to emote more clearly. Derrick hopes to eventually use the respirator on the design (and given how Malware's design evolved...).
Eventually the executives said there were too many alien transformations, so Whampire is the last new alien the show is going to introduce.
They were also at some point "mandated to have less transformations per episode going forward."
Fan Nickname: Dimension 23 SevenSeven is now commonly nicknamed Twentythreetwentythree by the fans.
Flip Flop of God: Due to Derrick Wyatt's discord with some of Dwayne McDuffie's adds in Alien Force, some of his statements turn out like this. Most notably, he removed the function that made Ben able to learn instantly what his aliens could do, and retconned Goop's Hollywood Acid (that had been stated by Dwayne to be his way to digest food) into an Omnitrix's glitch.
Also, Psyphon's origin. Dwayne McDuffie described him as being from one of planet Vilgax conquered, while Derrick Wyatt made a Shrug of God that he was possibly a cyborg or an android made by Vilgax.
Man of Action Studios was very clear on the fact Enoch did survive the Lotus-Eater Machine in his last appearance in the Original Series (though it took him several years to recover), and the sequels so far confirmed it by having him making a cameo in Ultimate Alien. When asked if he would be back, Derrick J. Wyatt merely answered he was dead.
Derrick has also confirmed David Kaye will voice Cannonbolt, John DiMaggio will voice Humongousaur, and Dee Bradley Baker's still voicing Spidermonkey. One can imagine Dee is breathing a sigh of relief, since he's said "voicing Humongousaur hurts his throat."
Derrick has confirmed that Corey Burton is now voicing a new villain named Malware as well as Brainstorm. Burton also reprises his role from The Secret Saturdays as V.V. Argost.
Kari Wahlgren reprises her role as Charmcaster, and also voices Viktoria.
I Knew It: Many, many fans had guessed that the reason Ben doesn't use Feedback anymore was because Malware had a part in it, most guessing that he flat-out destroyed the form, which is exactly what he did in "Showdown Part 1".
Jossed: Many figured Phil died after his first appearance in the original Ben 10 series. This series confirms that he's actually, for all intents and purposes, alive and well, albeit suffering from a split personality.
Lying Creator: Derrick J. Wyatt got mistaken for this due to "Store 23" featuring present Feedback, despite him stating several times he wasn't in the new Omnitrix. It was actually a diffusion error: that episode was suppose to take place after "Showdown Part 1" and "Part 2" where Ben would reacquire Feedback 
He also states that Zombozo was no longer a JokerExpy. When Zombozo shows up in "Special Delivery", he still uses the same Joker-esque gadgets from Ultimate Alien rather than his more supernatural powers from the Original Series. To be fair, his personality is less like the Joker now, although it's also not the same personality he had in the Original Series.
Way Big's ability to shoot cosmic rays was stated to be caused by an Ultimatrix glitch that wasn't present in the current Omnitrix. Yet he still uses it against Malware at one point.
Derrick said Steve Blum wasn't reprising any previous roles. In "Vilgax Must Croak", he plays Vilgax.
As of "Mystery, Incorporeal", he's also back as Ghostfreak.
Albedo was stated by Derrick to no longer possess the transformation ability gained in Ultimate Alien, instead relying on an Omnitrix again. In the show however, Albedo explains that he does still have it, and that his Omnitrix-looking device is merely a stabilizer to help him maintain his transformations longer.
Though given that a viewer would only know that in light of a mere three sentences of dialogue, this feels more like a mistake than a lie.
Many aliens who were played by Dee Bradley Baker (even those who themselves were replaced by Dee) have been replaced by a different VA (such as Cannonbolt being played by David Kaye), though Dee still plays a few (Spidermonkey, Water Hazard, Lodestar.).
Meagan Smith, Gwen's 10-year old actor, is not reprising her role, meaning that Ashley Johnson is playing both versions.
Azmuth is now voiced by René Auberjonois, having been voiced by Jeff Bennett during Alien Force and Ultimate Alien and by Robert David Hall in the original series and Destroy All Aliens.
David Kaye replaces Powers Boothe as Sunder. He also replaces Jeff Doucette as Thumbskull and Tim Curry as Joseph Chadwick in An American Benwolf In London, due to Tim Curry being sick at the time.
Grandpa Max was recast in the French dub after the first few episodes because the original actor passed away.
Yuri Lowenthal, normally known for voicing heroic teenagers, plays several aliens that are a bit different from what he's known for. The best example is Kickin' Hawk, a much larger and more muscle-bound character than, say, Simon.
Corey Burton, well-known for playing antagonists and wise men, plays store clerk and Butt Monkey Mr. Baumman in this show.
Along with Vilgax, a role that Steve Blum reprises, he also plays Hobble, who essentially amounts to the Butt Monkey of "Vilgax Must Croak".
Tara Platt as Ester, who isn't an older, serious-minded woman.
Promoted Fanboy: While Derrick got to do some design work on the previous sequels (SevenSeven, the Vreedles), he makes it clear that he's glad to work as the main art designer on his Formspring.
Recycled Script: And how. Sometimes, it really makes you feel like they took the idea to make the show more like the original series a bit too litterally:
"Hot Stretch" involves aliens with hight body temperature attempting to use a machine to raise Earth's temperature so it would be livable to them. Season 3 of Ben 10: Alien Force had an episode with Vulkanus attempting to do exactly the same thing with the same purpose.
While not identical, "Of Predators and Prey" has a lot of similarities with Vilgax's first direct encounter with Ben, down to Ben getting captured and the ship exploding at the end.
"Outbreak" involves Dr. Psychobos stealing a piece of the Omnitrix, resulting in it transforming the others instead of Ben. This seems like a mix of "Dr. Animo and the Mutant Ray" (where Animo had stolen the Omnitrix's faceplate) and the Ultimate Alien episode "Inspector 13" (where the Omnitrix, after being hacked by a villain, ends up turning Kevin and Gwen into aliens instead of Ben).
"Many Happy Returns" isn't a recycled script in itself, but the opening scene with Ben saving a girl from fire is basically lifted from a similar scene in episode 2 of the original show... only with Rath instead of Heatblast. Possibly a Mythology Gag.
"Special Delivery" has Psyphon trying to get his hand on a dwarf star, a device that is practically identical in its effect to the Forever King's Sub-Energy in the original show (except it works better). Plus, Ben defeats him by scaring him with Toepick, practically the same way he defeated Zombozo with Ghostfreak in their first fight. Oh, and Ben wrecked Mr. Baumann's car just like Kevin's. Seriously, it's like they tried to use as much old ideas as possible to make a new episode.
An episode has Ma Vreedle threaten to destroy Earth if he son isn't brought back to her... which was exactly the premise of the episode that introduced Attea, Emperor Milleus and Alien X.
Something Zombozo This Way Comes is almost entirely based on Original Series episode Last Laugh, down to copying the ending where Ben scared Zombozo into leaving (only with Toepick instead of Ghostfreak).
Role Reprisal: After a few years since the first series, Steve Blum finally reprises his role as Vilgax, as well as playing Zs'kayr again.
Running the Asylum: Aspects of this show up from time to time, mostly in characterization and design aspects.
Special Effects Failure: There's a sequence in "The Frogs of War Part 1" where Fourarms charges at some Inkurseans, who just stand there not firing or moving as he knocks them over.
Throw It In: Derrick says Psychobos' Catchphrase ("And I use that term loosely...") was originally just said once. It was when Eric Bauza, his actor, started putting it in inappropriate areas that they decided to make it his catchphrase.
What Could Have Been: The alien dog that used to be Khyber's that was adopted by Kevin was planned to be in "Frogs of War", but the scene had to be cut for time.
Zombozo's escape in "Something Zombozo This Way Comes" was to have him land on Anur Transyl, thus possibly giving him some sort of role in the arc with Zs'Kayr in it, but they scrapped it.
Word of God: The reason why Bullfrag looks different from other Incurseans is because he's a genetically optimal (completely healthy and fit) specimen, and most Incurseans have poor diets.
Several aliens have sound effects that accompany their speech or movements: Spidermonkey has monkey-like chatter; Crashhopper's speech and jumps include cricket noises; and Shocksquatch has a crackling undertone to his voice like electricity. Liam's speech is littered with chicken noises, but Kickin' Hawk (who was based on Liam) has hawk screams instead.
We discover in one episode that Rook's given name is Blonko; his people put their surname first, like another alien species, the Bajorans. (Like most Asian-ethnic people in Real Life, as well).
Upchuck's species, Gourmands, come in two different variants, Murk and Perk. These correspond to the two different designs that Upchuck has had in the original series and the sequels. The original series' Upchuck was a Perk which is a reference to Tom Perkins who designed Upchuck in the original series, while the sequels' design for Upchuck is a Murk which is a reference to Glen Murakami who was an executive producer for the sequels.