Funnily enough, way back during Alien Force Word of God's explanation for why Kevin didn't absorb energy anymore was that he was "scared to," which suggests they already had this planned. Several sources suggest they would have used it in season 3 of Alien Force, but were unable to because of Executive Meddling.
Charmcaster is seen using her bag from the original show again.
And Ben finally acknowledges his character regression over the last few seasons.
Likewise with the first live action Ben 10 movie and the villain Eon. Plus why this series isn't following the first series future timeline. (Alternate Universe)
Broken Base: On many, many subjects. The Ultimate Aliens especially. Others include whether this series is good as the two before it, whether it's successor will be better or worse, and so on and so forth.
Ben's immaturity in Alien Force is heavily downplayed, making him a bit smarter and more responsible as he was in the first two seasons of that series. The result is more of a comfortable mixture of the traits that people liked in Alien Force, but still kind of prone to poorly thought out and emotional responses the first series had.
Vilgax, while not as monstrous as he was in the initial series, is made into a Magnificent Bastard. He successfully tricks Diagon!
Complete Monster: Aggregor is an Osmonian warlord who was wantonly murderous in his quest to achieve omnipotence. Aggregor killed aliens by absorbing their energy and matter to gain their powers. Generally this caused his victims to turn into desiccated husks, but for his plans to become powerful enough to reassemble the Map of Infinity, he turned five aliens into energy and absorbed them into himself. Aggregor killed Magister Prior Gilhil by stabbing him in the back, killed two other Plumbers by sucking them into space, and absorbed the life and powers of a pacifistic alien just because he could. His two most vile crimes, however, were when he nearly destroyed an entire inhabited world by stealing a component from the device that kept the planet from breaking apart, and when he tried to kill and absorb a baby alien capable of Reality Warping to complete his ascension into godhood.
Continuity Lockout: If you haven't seen either Alien Swarm or Race Against Time, you won't really understand the context regarding the Swarm, Eon, or the Hands of Armageddon.
Conflict Ball: Ben suddenly deciding that it's absolutely necessary to kill Kevin in the first season finale, even though he never focused on killing any previous enemies (including ones which were much more of a threat than Kevin), and Grandpa Max points out that he's acting out-of-character in the show itself.
Evil is Cool: Aggregor generally is considered one of the best things that came out of this show amongst the fans. Many were genuinely disappointed when Derrick J. Wyatt said he had no plan to bring back the character in Omniverse.
Ultimate!Kevin's dialogue with Ben, in the beginning of the season finale, sound completely wrong taken out of context.
Franchise Original Sin: The next series gets a lot of complaints about overt focus on first-series continuity, Pandering to the Base, and script-recycling. This series seems to have had those problems before Omniverse, given the almost suspicious abundance of first-series elements, such as an appearance by one-off Zombozo, a storyline involving a Kevin who is a composite of Ben's aliens, as well as a guest appearance by the original, 10-year-old Ben, indicating that the next series only heightened these flaws.
Growing the Beard: If you consider this show another season rather than a separate show. Ultimate Alien had a clearer idea where it wanted to go with its first arc, filler episodes were not half as frequent as they were in Alien Force, and managing to strike a clean balance with Ben's personality. Season 2 would be far less lucky.
In the episode "Revenge of the Swarm", Ben and the others find out from a janitor that Elena's father had died. Kevin asks if he's telling the truth, the janitor replies "Anyone can die anytime". Wouldn't you know around the same time the episode aired Dwayne McDuffie passed away?
Also, Jennifer Nocturne developed Stockholm Syndrome, even to the point of having feelings with Carl Nesmith (Captain Nemesis). Five months later, Kristen Stewart, whom Jennifer Nocturne is an Expy of, cheats on Robert Pattinson, having a brief affair with director Rupert Sanders. Boy did the show predict what would happen to Kristen Stewart...
It's revealed in The Forge of Creation that Alien X was locked and one of the reasons was to prevent other characters like Albedo from accessing it in case they got hold of Ben's Omnitrix. Then come Ben 10,000 Returns, when Paradox explains an alternate universe where Albedo did use Alien X, only to stay motionless for a year.
When asked if Zombozo would return, Dwayne McDuffie said "not if he knows what's good for him". One of the first villains confirmed for Omniverse is Zombozo. Looks like he doesn't know what's good for him.
Will Harangue is what a Jonah J. JamesonExpy, the only real difference beside his look being that he is an anchorman instead of a newspaper director and is pursuing Ben, a character created by Man of Action, instead of Spidey. A few years later come Ultimate Spider-Man, which Man of Action is working on... and where Jonah J. Jameson is portrayed as an Anchorman instead of a newspaper director.
Parodied with Clone Ben and Kevin in a car in "Duped".
Arguably Cash and J.T. in "Reflected Glory". How many times did they have their arms around each other again?
Ben and Kevin again in the season finale ending "Absolute Power". The two have their little reconciliation, Gwen steps in to ask who wants to go with her to explain to her parents about their destroyed house, and Kevin promptly asks Ben if he wants to go to Mr. Smoothie with him. The two walk off together; cue credits.
Gwen and Charmcaster in "Where the Magic Happens".
And again in "Couples Retreat", where Gwen rags on Kevin for failing in his boyfriend duties all episode, and is a lot more emotionally invested in saving Charmcaster from being used by Darkstar. Ah, another good ol' Ben 10Relationship Writing Fumble!
It's the Same, so It Sucks: There were some complaints that it was too similar to the previous series, due to sharing the same general tone, artstyle, and format.
Memetic Mutation: Kevin's infamous "When two (X) love each other very much..." sentence.
Moral Event Horizon: Alot of dark stuff happens in this show, but one case is unanimously agreed upon: Captain Nemesis becomes the first successful hands-on murderer in the series. He kills several people, including a random motorist just to steal his car. Even his Pet the Dog moment at the very end doesn't bring him back across the line.
Eatle's in a similar situation, only he isn't as hated as Fasttrack since his design is a lot more unique. Regardless, he was heavily redesigned◊ in Ben 10: Omniverse to look more like an actual beetle and less robotic (a fault he shares with a lot of Ultimate Alien aliens), which may earn him some brownie points.
Four Arms was given a design that was either a Shout-Out to Goro or the Green Martians, complete with very little clothing and a ponytail. The fandom (and Derrick) weren't pleased, and he was given a more traditional look in Ben 10: Omniverse with a Badass Moustache, which while still divisive, wasn't as loathed as his design here.
Ripjaws was an Alluring Anglerfish with More Teeth than the Osmond Family in the original series, Here, he has a more catfish-like face and fish lips that may have been an attempt to make him less Nightmare Fuel-y. However, fans weren't pleased at all, and Derrick has promised repeatedly his Omniverse design will be much cooler.
Rescued from the Scrappy Heap: This show's version of Eon was generally better-received than the movie version. For some reason, Derrick J. Wyatt still decided his episode to be non-canon.
Despite undergoing Character Development, Julie has once again began to become this, due to her having to Took a Level in Jerkass due to her unable to stand Ben's fame going into his head, breaking up with Ben the first time as a result before getting back together with him (and then breaking up with him again in the Omniverse series) before finally joining an evil cult that she thought was a charitable service and even initially refusing to listen to Ben when he suspects the cult of being evil. As a result, her Omniverse appearances, which were her last appearances in the Ben 10 franchise, have been nothing more but a Take That, Scrappy! to the character.
Trumbipulor didn't exactly impressed anyone during his small appearances. Most fans agree Omniverse did a mistake by bringing him back later.
Fasttrack is one of the less popular aliens, being viewed as a inferior replacement to Ensemble Darkhorse XLR8. He ends up being Put on a Bus in Omniverse.
No matter how "randomized" her DNA is, it can be a little unsettling to notice how much Eunice and Gwen favor... or worse, how she and Ben resemble each other. Or, for the Ben/Gwen shippers, she could be a dream come true.
Hive Elena's offer to be more like Gwen as a girlfriend if that will make Ben happy.
The fate of Victor and Elena Validus. Turns out Victor died offscreen in an experment and that the Hive used Elena as a secondary Queen to survive, making her believe everything they do is just what she wants them to do and she's in control. Ultimately, unable to allow Ben's death, she manages to regain control and kill herself along with the Queen. What makes it even more of a Tear Jerker is that The Stinger reveals it was in vain as the Hive survived.
Less of one now—Turns out Elena somehow survived too and is even crazier. She brought two buildings to life to try and kill Kevin when he got too close to figuring out she was impersonating Julie.
Less of one or MORE of one? Death is probably preferable to madness.
"Prisoner 775", everything about the title character in general. The worst part is when he breaks down at the end and begs Ben to put him out of his misery and let him rejoin his dead family.
Charmcaster's crying moments in "Where the Magic Happens", "The Enemy of my Frenemy", AND "Couples Retreat". Charmcaster's character arc was depressing to a ludicrous degree, especially since it was left unfinished and she's left alone.
The ultimate fate of Kwarrel, the prisoner who taught Kevin to control his anger.
In-universe, Kevin attacking Gwen and then holding off for what they had, in his words causes her to cry for the first time in the series.
In "Ultimate Sacrifice" Ben was going to die willingly so that some of his Ultimate forms could escape the Ultimatrix and be free.
Jennifer Nocturne's backstory in "To Catch A Falling Star".
In "The Ultimate Enemy", Old George's death.
They Changed It, Now It Sucks: Just like fans of the original series had this reaction toward Alien Force, there are a good number of Alien Force fans who hated the changes made in this series.
Old George was a fairly well-received character, with an intriguing air and mystery to him, but he dies before we can learn much more about him or his backstory, including the question of how he's immortal.
Ben deciding that Kevin needs to die in order to stop him is arguably this, as Ben makes almost no effort to resolve the situation peacefully. One attempted murder on a guy who obviously had it coming (before this it had been brutal beatings and they had apparently never caught up until this point), and Ben's all for killing him.
The reasoning behind Charmcaster's Face–Heel Turn in "Enemy of my Frenemy". Seriously, Charmcaster? You think your father would WANT you bringing him back to life at the cost of 600,000 living souls?
Darkstar in "Couples Retreat". You can't remember a four-letter word? Really?