The Avengers (2012) has both Black Widow and Hawkeye as original members, even though both characters joined later rosters in the comics. Additionally, the Chitauri weren't created in the comics until 2002, and didn't join the mainstream Marvel Universe until 2013. In the movie, they, along with Loki, are the first threat the Avengers have to stop as a team.
Captain America also is part of the team from the beginning as he's found frozen in the ice at the end of his first solo movie by S.H.I.E.L.D. as opposed to the comics where in the now famous fourth issue the already established Avengers found Cap before the latter joined the team immediately.
Captain America from his second solo move on draws heavily from Ed Brubaker's work with the character that started in 2004. The most prominent aspect of his work in the MCU is his reinvention of the Winter Soldier, Bucky Barnes. Bucky was changed from a long dead Kid Sidekick to someone who was kidnapped by the Soviets in World War 2 and turned into an assassin with a metal arm.
Ultron is the main villain of Avengers: Age of Ultron, and is accidentally created by Tony Stark. In the accepted comics canon, Hank Pym (the first Ant-Man) created Ultron, but Hank had not even been introduced at this point in the MCU.
The Avengers had already been published for about a decade when Thanos first appeared in 1973. In the MCU, Thanos has essentially been the franchise's Greater-Scope Villain since the first Avengers movie, where he was revealed to be the Man Behind the Man in The Stinger.
In the comics, James Rhodes didn't appear as part of Iron Man's supporting cast until 1979, and didn't become War Machine until 1992. He's part of Tony's supporting cast from Day 1 in the first Iron Man movie, and becomes War Machine in the very next movie. In this continuity, he effectively predates a bunch of characters who have been around a lot longer in the comics, like Spider-Man, Doctor Strange and Hawkeye.
Inverted with Spider-Man himself. In the comics, he predated Iron Man and the formation of the Avengers, and was in fact, probably the only major Marvel hero at the time not to be a member of the team when the book first launched. Because Spider-Man's movie rights were off-limits during the first two Phases of the MCU, he doesn't show up in the movies until several years after the Avengers have already been formed (and when he is, they go back to the beginning and thus give him an Age Lift in comparison to the others). In fact, Peter Parker's idolization of the Avengers (especially Iron Man) is a plot point.
Iron Spider and Tony's mentoring role are also a case, as these are things that didn't happen until Peter was married and in his twenties. Here, he's 15 when he meets Tony and the Iron Spider suit is gifted to him six months later.
As an Expy/Race Lift of Mary Jane Watson, Michelle Jones, A.K.A "MJ," would count as well, since she's introduced as Peter's high school classmate in Spidey's first solo MCU outing, while Gwen Stacy has yet to be introduced in this continuity.
Also by extension, pretty much every other teen character and young hero in contrast; Peter was a grown man by the time other teen heroes started showing up, and is Older and Wiser than most of them now. Here, Peter's at least decade younger than Jessica Jones (whom he went to high school with) and Daisy Johnson (who is almost a decade younger than him in the comics), and is the same age/younger than such heroes like the Runaways and Cloak and Dagger.
Shuri is present from the very beginning of Black Panther (2018), even though she wasn't introduced until the 2005 run of the comics. Same goes for the Dora Milaje, one of whom even appeared in Captain America: Civil War, despite not existing in the comics until The '90s. Somewhat a Justified Trope though, as in both cases, the characters were depicted as having always been part of Black Panther's cast; later stories set during T'Challa's early years or flashbacks to previous eras in the comics have depicted them as being around the whole time, and just never mentioned/seen during these previous stories.
Even if the Thunderbolts movie includes none of the original formation, U.S. Agent, Yelena Belova, Winter Soldier, Ghost and Taskmaster were members of later incarnations. No matter if with a few caveats (the Yelena who joined the Thunderbolts in the comics was actually a disguised Natasha Romanoff, and both Ghost and Taskmaster in the MCU are reimagined Gender Flips, with the former having a Race Lift).
