These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ensemble Darkhorse: Lucky Girl, who is ironically one of the leads in disguise. Her nemesis Charmcaster qualifies on the villain side of things.
Naturally, some of Ben's aliens are more popular than others, but the one who takes the cake (from the original series, at least) is Heatblast. He's enough of a dark horse than a Ultimate Alien DVD was titled the Return of Heatblast.
XLR8 is also pretty popular, which makes it extra baffling that they went and made Fasttrack.
Buzzshock and Articguana, two of Ben 10,000's aliens, are surprisingly rather popular among the fanbase, despite the fact neither have ever appeared outside of that episode aside from a cameo in Ultimate Alien's theme. Articguana is finally used by the 16-Year-Old Ben in Omniverse, and Buzzshock appears even later.
Sixsix, a minor villain from early in the series, quickly became beloved by fans due to essentially being the Ben 10-verse's equivalent of Boba Fett. He was so popular that not only was he brought back later on but the sequel series introduced his family made up of his equally badass brother and two sisters, changing him from a one-off mook to a series mainstay.
Evil Is Cool: This show is a master at creating awesome bad guys. Vilgax, Kevin, Ghostfreak, Hex, Charmcaster, the Forever Knights (especially the Forever King), Sixsix and his family, and nearly all the other villains (with the exception of Sublimino) who made up the Negative 10 could count.
Franchise Original Sin: One complaint about the sequel series is how redundant some of Ben's aliens can be. The first series has many aliens who, while having unique abilities, some have similar advantages to one alien that leave another alien functionally redundant (particularly Benvicktor/Frankenstrike, who on top of having super strength, has lightning abilities), indicating that there were ability and redundancy problems even before the sequels.
A lesser example, but one of the major criticims done to Alien Force was (amongst other things) about the Plumbers being inexplicably active again despite being stated to have disbanded in the first series; Big Fat Alien Wedding, while not explicitly stating the Plumbers were still active, made mention of a war between them and the Sludgepuppies that was apparently still going on (the whole point of the episode was to end it), suggesting at least some of them kept fighting.
Fridge Logic: So, if Ben was so desperate to unlock the secrets of the Omnitrix, why didn't he just use Grey Matter's intelligence to do so? Amusingly, Kenny in "Ken 10" does think to do this.
Remember that ending in Gwen 10 where the Omnitrix ultimately ended up on Grandpa Max? Several episodes later, some alien named Xylene, a person from Max's past, revealed that the Omnitrix was originally for Max. But thanks to the fact that Ben's DNA was close to his, and Ben was the one who discovered it, it ended up on him.
In the end of "Kevin 11", Ben offers Kevin to join him and become allies. Soundfamiliar?
In "The Big Tick", while trying to figure out what his new alien does, he lists powers of aliens he will receive in the future.
I Knew It: Some guessed that Ghostfreak would turn evil when they found out the Monster of the Week was an Ectonurite in "Ghostfreaked Out", despite some sources saying that it was a completely separate Ectonurite. When the episode aired, the truth became apparent after a nightmare detailing Ghostfreak telling Ben to let him out of the watch, and then subsequently escaping the watch after dealing with Zombozo's unemployed henchmen.
Moral Event Horizon: Kevin was going to crash two trains together, one full of cash, the other full of innocent lives. Most of the other antagonists before this were more formulaic in their general supervillainy, but this? That's going too far.
Vilgax destroys the planet where all of Tetrax's race lives, killing hundreds of innocent lives for no reason other than to test his brand new toy.
And Ghostfreak wanted to plunge Earth into darkness, the result of which is shown to be horrifying mutations of all living things.
Also note, that was just a side effect of his plan that he didn't even care about.
Zombozo gets his by kidnapping a 10 year old girl and draining her of her energy until she's nothing but a shrivaled husk of her former self, speaking of it so lightly that it's implied it's not the first time.
As if it wasn't clear that the Forever King is more evil than Enoch, he deliberately leaves Enoch trapped forever in his Lotus-Eater Machine just to spite him for not getting the Omnitrix.
My Real Daddy: Since this was the only series produced by Man of Action, there are a sizeable amount of fans who consider it alone canon and regard the various sequels as Fanon Discontinuity.
Older Than They Think: There really was a secret organization called the Plumbers - Richard Nixon's private police who did the illegal surveillance of the Watergate hotel.
The Scrappy: Kai Green does have some fans, but mostly she has a very sizable hatedom, due to her only episode portraying her as a rather unsympathetic character who Ben fell in love with for no real apparent reason before she rejected him rather callously (and unlike Julie, no effort was made by the writers to rescue her from the Scrappy Heap) and being an obstacle toBwen.
Seasonal Rot: The third season is generally considered the weakest due to less impressive episodes and overall story arc than the other seasons have.
They Changed It, Now It Sucks: Race Against Time. Dear lordy, Race Against Time. Some fans were NOT happy when they realized the aliens were not voiced by the original voice actors.
They Wasted a Perfectly Good Character: At the end of the third season, Ben gets three new aliens, each based off a different monster. A werewolf, a mummy, and Frankenstein's monster. Despite all being pretty cool, they don't appear at all for the rest of the series, and it isn't until an alternate timeline episode in Ben 10: Ultimate Alien that any of them reappear. They aren't even properly named, being referred to as "Ben*monster name*" in the credits. It took until Ben 10: Omniverse for them to even be given proper names.
While Ghostfreak is a cool villain by himself, you could argue he was wasted motivation-wise: When he first escapes the Omnitrix, his dialogue implies he is motivated by revenge toward Ben for having him prisoner in the Omnitrix for so long. This idea is completely dropped right in the same episode, and for all his next appearances in both this series and the sequels, he is portrayed as an generic "I want to conquer the Universe" villain.
Viewer Gender Confusion: Ben 10's character, Ripjaws, is part deep-sea creature and merMAID, so he might seem like a female, but he's actually a male.
Visual Effects of Awesome: "Destroy All Aliens" has particularly impressive CGI effects, with the Galvanic Mechamorph's fluidity being especially noticeable.