Season 2 had several episodes dedicated to going over the backgrounds of White Tiger, Nova, Power Man and Iron Fist, which can be viewed as being (partially) in response to fan complaints about how Spidey is expected to trust them with everything when he knows nothing about them other than their names and aliases.
Spider-Noir and his universe's version of MJ received a decent amount of Ship Tease, which may have had something to do with the mass amounts of complaints over MJ's barely existent presence in the show.
Deadpool's inclusion could be looked at as this, considering a lot of people said this show's humor would've worked better in a Deadpool cartoon rather than in a Spidey cartoon.
Some fans, while receptive, were rather confused by the various changes done to the Peter Parker character model. In "Iron Vulture" some of his dialogue indicates that the events of the first three seasons took place over two or three years, justifying the change as Peter was only 15 when the show started and more than likely hadn't finished puberty yet.
Nova and Fury, two of the most hated characters in the show, mysteriously disappear at the start of season 4 and only reappear near the end of the season, and in extremely minor roles to boot. While there is a plotline involving finding them that same season it's rarely ever touched upon. Their absence is no doubt a result of the aforementioned hatred they've received.
Given how disliked 3/4ths of Spidey's original team was in season 1 their phasing out in season 3, and getting replaced with more spider themed charactersnote Flash Thompson as Agent Venom, Amadeus Cho as Iron Spider, Miles Morales, Scarlet Spider, Julia Carpenter as Madame Web, Mary Jane Watson as Spider-Woman, special mention going to Harry Osborn as the Patrioteer was more than likely this. Even the non-spider recruits gained in the season, Ka-Zar and Zabu, Cloak and Dagger, Squirrel Girl, Triton, even Rhino and Sandman, were well received.
Arguably the treatment Sandman gets after his first appearance is this. Prior to the show it's stated that he was left on an uninhabited island by S.H.I.E.L.D. ...but for unknown reasons. The reason was implied to be because he and his powers were so dangerous, however the facts that he didn't seem all that much older than the team and several things pointing (intentionally or not on the writer's part) that he didn't originally suffer from the psychosis he displayed in his first episode proper, but rather he went full on Go Mad from the Isolation due to being on the island for an unknown amount of time (possibly since he was a child given how young he looks}... Well, let's just say fans didn't react very well, and the episode is considered by many to be one of the bigger examples of Fury's Designated Hero status. Subsequent episodes however go on the humanize Sandman further, and showing him attempting to be a hero (if not just simply a good person.) Eventually in Season 4 Spidey takes him to a relatively uneventful area where he can live peacefully while also giving the choice to potentially join his team one day, effectively ending his character arc for now. Season 4 also introduced fellow elemental Hydro-Man who was in a similar position as Sandman but is most definitely a immoral psychopath through and through. He also appears to be significantly older than Sandman, which arguably justifies Fury's actions against Sandman on a pragmatic level.
MJ returning near the end of Season 4, as well as having a major role, via being possessed by Carnage, and then being cured in a way that allows her to use its abilities as Spider-Woman, seems to have been brought on by the season-and-a-half full of fans complaining about her being Put on the Bus.
The series finale has Spider-Man being forced to save the day on his own after his SHIELD tech is destroyed and all of his teammates are captured. Aunt May even gives him back his original web-shooters and says that he didn't need S.H.I.E.L.D. to be a superhero. as he already was. He later graduates from the S.H.I.E.L.D. Academy and is given Fury's blessing, and the series ends with him returning to solo superhero work, essentially bringing him back to the status quo people know and love from the comics.
