In its early days, the Ultimate titles were a big success and overshadowed the original titles. This was especially the case with the Ultimates, which had far greater success than the relatively obscure Avengers (remember that there was no MCU at this point yet). In fact, let's just say that the first two Ultimates miniseries, the most beloved ones, coincide with the Avengers' Dork Age under Chuck Austen. The process was eventually reverted in later years, mainly by the work of Bendis (in New Avengers) and Mark Millar (in Civil War).
Ultimate Nick Fury has completely overshadowed the original white version due to his deliberate Comic-Book Fantasy Casting as Samuel L. Jackson, which became reality when Jackson started playing the role in the MCU. He has been used in all adaptations of the character since then (for reference, the last Marvel adaptations with a white Nick Fury were the Marvel Ultimate Alliance duology and Spider-Man: Friend or Foe). In the main universe, there is a son of the original Nick Fury who also uses that name and who looks this way (so, for all purposes, it's like having Ultimate Nick Fury around).
Ultimate Hawkeye's suit looks like sportsman gear instead of the classic purple suit with the Wolverine mask. Ever since it was used in the MCU, it has carried over to the Avengers, Assemble! TV series and finally the main universe.
Ultimate Captain America's suits are much more "tactical" with padded armor in contrast to classic Cap who still essentially wears mostly tights. As with Hawkeye, the MCU took heavy inspiration from this for most of movie Cap's suits.
Hobbie Brown, the original Prowler, has long faded into obscurity. Ultimate Prowler is Aaron Davis, Miles Morales' uncle, and was eventually moved to the prime Earth as well. In either universe, Davis is THE Prowler nowadays. He also appears in Spider-Man: Homecoming and Spider-Man: Into the Spider-Verse.
Have you ever heard about the original Bombshell? No? A blonde and muscular stoic terrorist, who used actual bombs? Not ringing any bells? Don't worry, she only appeared in the short-lived Hawkeye miniseries in 1983, and then suffered the Chuck Cunningham Syndrome. Bombshell only took the name and the explosions motiff from her, and nothing else. She was brought to the mainstream comics alongside Miles' cast, and joined the Champions in 2019. And no, nobody asked about the "original" Bombshell during this.
Author's Saving Throw: In Doctor Doom's last adventure in Ultimate Fantastic Four, he was stranded in the zombieverse. Loeb seems to have skipped that part as he gave no explanation about his presence in Ultimates 3. And then he was killed at the end of Ultimatum. This was all fixed in Ultimate FF, with the return of Van Damme, and the clarification that the guy used by Loeb was actually Mary Storm posing as him.
Spider-Man and Wolverine have a "Freaky Friday" Flip, and they both go through several bizarre things. Even Bendis himself appears at the start of the episode, accepting how bizarre it was, and that he could not milk more than two episodes from that idea.
In one of the last issues of Ultimate FF we learn about an alternate universe, which seems to be basically the same than the Ultimate one, except that the local characters are Anthropomorphic Animal Adaptations. It's as bizarre as it sounds and then some.
Ultimate Adventures. It was an odd Batman and Robin parody, and was never referenced by any other Ultimate titles.
Ultimate Nick Fury, so much that he is currently better known than the Caucasian mainstream version; he was even used for the movie adaptations albeit his personality there is nothing like his Ultimate characterization.
The Ultimate Jessica Drew became a pretty big one.
Pyro, probably due to his interesting design.
Cinema Blend described Ultimate Tony Stark as an "alcoholic, arrogant, and slightly detestable version of Tony Stark who you still couldnt help but be charmed by and root for."
The Marvel Zombies were created in Ultimate Fantastic Four. They were so successful that they got their own miniseries (but as they were from an alternate universe to the Ultimate universe, they are not considered part of Ultimate Marvel imprint, regardless of their editorial origin).
Miles Morales is perhaps the most famous example in the Ultimate Universe, and one of the few characters to migrate over to the 616 universe after the events of Secret Wars (2015). While still a fairly recent creation, he already has a prominent presence in pop culture, with a central role in an animated film and being referenced in the MCU, several appearances in cartoons, video games (mainly the 2018 PS4 game), a young adult novel, and other merchandise, establishing himself as a new yet integral part of the overall Spider-Man mythos.
Harsher in Hindsight: When Magneto returned, Nick Fury started setting up defenses in the White House. "The White House is gonna be a virtual fortress by the time I'm finished with it. Absolutely secure against both post-human and nuclear attack". And it did work... until the Maker blew up all of Washington DC.
When the Ultimate Universe was first started,there were some rumblings and rumors among fans that Marvel was going to use it to reboot/replace the mainstream universe. Years later, this ended up basically happening over at DC.
Ultimate Power, being drawn entirely by Greg Land, has a lot of his... "unique artistic touches" present throughout.
Reed Richard's FaceHeel Turn in "Ultimate Enemy", and his explanation for his motives in particular at the end of the trilogy, comes across less as an emotionally fragile genius having a breakdown as much as him throwing a tantrum.
Older Than They Think: The Maker is a villain who is a Knight Templar who works For Science! and is willing to establish a scientific utopia by any means needed, no matter how evil and destructive. Although the most successful and popular one, he was not the first character in the Ultimate Marvel universe to fit this description: George Tarleton from Ultimate Vision was another contender.
Similarly, Ultimate Wolverine is also widely hated both fans of his mainstream counterpart and of the Ultimate Universe for his creepy sexual acts and obsessions. See Values Dissonance below for more details.
Seasonal Rot: The Jeph Loeb era (from Ultimate Power until the end of Ultimate X) in general and Ultimates Volume 3 and Ultimatum in particular, and the start of the rot period, and most definitely the height of it. It's easy to see why Marvel relaunched the line as Ultimate Comics afterward. Ultimate Spider-Man is usually exempt from this, though, and hasn't ever really had been hit with the trope, with the worst of it being volume 3's Broken Base regarding Miles Morales.
After the line's huge success in its early days, Marvel started incorporating some of its stylistic trademarks (e.g the more cinematic pacing and storytelling) into its main universe (under the pens of Mark Millar and Brian Michael Bendis to boot), thus leaving the Ultimate Universe without a distinct voice. This is one of the main reasons that led to Ultimate Marvel's sales decline in the mid-late 00's.
Another initial positive aspect of the Ultimate universe was that it was a fresh start, without the Continuity Lock-Out that the mainstream Marvel universe had after so many decades. This aspect was lost simply by the passing of time, as the Ultimate universe would eventually get to a Continuity Lockout of its own.
In the climax of the first Ultimates series, Captain America refused to surrender to an alien conqueror that was Piggybacking on Hitler, and said that the A on his costume "does not stand for 'France'". The scene was a hit because of its Double Meaning: it pointed to the armistice of June 22, 1940, where the French government surrendered to the Nazis in WWII, but it was also a subtle Take That! to modern France, as France had refused to join the US in the ongoing War on Terror. The effect was less effective years later, as the wars in the Middle East became less popular in the US and the backlash against France for not joining it became less noteworthy.
Signature Scene: The climactic fight between the Ultimates and the Liberators, specifically for showcasing almost every hero in Ultimate Marvel up to that point. It's even used as the page image for Ultimate Marvel itself.
They Changed It, Now It Sucks!: The portrayal of the X-Men and especially Magneto was heavily disliked since the majority of them were all made into jerks with very few likable characteristics and this ended up making their role as the "good" mutants problematic. Specifically, Magneto being made into a genocidal psychopath with none of the redeemingelements the mainstream version had was seen as a waste of a good villain, and which likewise made Professor X's mercy and willingness to try and redeem him seem especially pointless and suicidal. The twist at the end of Ultimatum, that the mutants are not a product of evolution, is likewise seen as a cheapening of their entire mythos.
They Wasted a Perfectly Good Character: Ultimate Captain Mar-Vell. A Kree soldier who defects to try and save Earth from Gah-Lak-Tus because he thinks we're interesting, showing himself to be smart, snarky (well, he was created by Warren Ellis), but openly good and decent, a rarity in the Ultimate Universe. But he was not incorporated as a regular character in any of the ongoing series, and just had roles in some crossover events. He was eventually killed in the "Hunger" miniseries.
Carol Danvers as head of S.H.I.E.L.D., given she was an air-force officer not used to running an intelligence agency, but she's far less morally compromised than Nick Fury. And then the writers proceeded to do absolutely nothing with that idea, and she was eventually booted out in favor of having Fury back in charge. She also never became a superhero like her mainline comics counterpart.
After Ultimate Power, Zarda of Supreme Power travels over to the Ultimate universe to "keep an eye" on the Ultimates. She proceeds to do nothing of any real value, before leaving again at the end of New Ultimates. Making this all the more baffling was that Jeph Loeb was the one who brought her there and then wrote her out again (a decisions which, rather infuriatingly, meant that they screwed up the plans for Supreme Power for nothing).
Ultimate Jessica Drew is the female clone of Peter Parker, a heterosexual man, and has his exact mind, memories, and feelings. Peter likes women, and so does she. As discussed by Spider Talk, this would open the door to an interesting exploration of gender topics, but it was never used beyond some limited scenes. Of course, she was a secondary character, and to treat the topic with the required depth she should have had a comic book for her own.
While it's status as canon tends to flip-flop, Ultimate Origins reveals that Richard and Mary Parker were killed by the Hulk after Banner's first transformation. Peter never finds this out and the dramatic potential of him confronting Banner/Hulk about this is never explored.
At every issue of Ultimate FF. But the last one takes the cake: Miles Morhames? The Ultimate Spider-Ham?
In the later third of Ultimate Power, a mishap causes the original Squadron Supreme to show up.
Who would have expected the fight between Wolverine and Hulk to be interrupted by Ultimate She-Hulk?
The Ultimate Galactus Trilogy featured Ultimate Misty Knight, a character who had not been used by Marvel since the 1970s. After this appearance, she was brought back into the mainstream Marvel universe as well.
Probably nobody expected the cops in All-New Ultimates to turn out to be the Ultimate take on Terror Inc. (or that such a team ever existed).
The biggest one is the normalization of incest in Ultimates 3 where the conversation between Janet and Steve Rogers about Wanda and Pietro as written is supposed to communicate Janet's acceptance and sympathy for the siblings' relationship as a modern idea of acceptance while Steve's horror indicates his old-fashioned nature. The problem is that the incest taboo remains in place for most societies across the world even in the 21st century, and it ends up making the writer look more than a bit creepy at best.
Ultimate Wolverine's creepy seducing of teenage and adolescent girls was intended to paint him as a "bad boy" and ladies' man, but especially after the #MeToo and Time's Up movements, he comes across as a creepy sexual predator and pedophile. His seduction and fixation on Jean Grey, who at the very least was of legal age, was bad enough but he later frags Cyclops to Murder the Hypotenuse and then lies about doing so to Jean. His behavior when he is trapped in Peter's body (a situation caused by Jean Grey because he tried to creep on her again) has him trying to take advantage of Peter's relationship with MJ to apparently do something lewd with her, making him come across as an attempted rapist.
This also applies to Tony Stark who openly seduces and sleeps with his interns and co-workers and where Wolverine at least gets some pushback, this is glorified as Ultimate Tony's usual playboy schtick, when today that kind of stunt would be seen as red flags and unbecoming of a supposed superhero.
At the end of the '90s, Marvel declared bankruptcy and their comics were underselling as a result of a general Dork Age that had gripped the Marvel Continuity since the '90s. Ultimate Marvel, especially under the pen of Brian Michael Bendis provided a refreshing spin and change of scenery, as well as a proving ground for alternative takes on familiar characters that were tentative experiments on the direction Marvel could go in the future.
Ultimates 3 and Ultimatum, by Jeph Loeb, were widely panned as bad works. It did not help that he was still coping with the death of his son and that he was not familiar enough with Ultimate Marvel. His work improved with New Ultimates and X, and the Ultimates and X-Men finally returned to their great quality when written by Jonathan Hickman and Nick Spencer.