The MCU's Spider-Man 3 has an Iron Man problem and the only way to solve it is by making Uncle Ben important to Peter Parker's origin story again. The tragically murdered father-figure to Peter Parker has traditionally been a major part of Spider-Man's origin, offering him the foundation of his entire heroic belief system (even beyond his eminently quotable "with great power..." line). But the MCU chose not to retread Spider-Man's origin after two reboots, with audiences already very familiar with how Spider-Man got his powers.
At the time, it wasn't a bad idea, because it allowed for an almost fully-formed hero to arrive into the Captain America: Civil War picture before stepping back into his own solo movies. But then the MCU filled the void left by Ben with Tony Stark and did the character a disservice, not to mention completely reframing Spider-Man's own story. Rather than becoming a hero inspired by the principles and morals of his uncle and cemented by his death, Peter Parker became Stark's pet project - a surrogate son he molded into his own image who naturally then mourned his death in Avengers: Endgame.
The problem with that is that Peter Parker has never had his own story to tell, as long as he's stood in Iron Man's shadow. His grief at the loss of Tony eclipsed any emotional response to Uncle Ben's death, which became nothing more than a historical footnote. And that is fundamentally a betrayal of Spider-Man's core and a hindrance to the MCU's version of the character's future. If there is to be one beyond Spider-Man 3, Peter Parker has to be allowed to move on from Iron Man and he should turn to his own past for the key to do it.
Uncle Ben's death wasn't just a sad origin story. Unlike the murder of the Waynes, which twisted Bruce Wayne with vengeance, Ben's death robbed Peter of his moral guide. In his absence, Peter's unspoken mantra would become "what would Uncle Ben do," which ran through both of the previous movie franchises, but his ghost also drove Peter in a more specific way that come back into play in the MCU's Spider-Man threequel. He was a warning for what might happen to Peter's family if it was discovered that he was Spider-Man. And given that J Jonah Jameson has just revealed Parker's secret identity to the world, that fear should be pressing again.
Spider-Man 3 should refocus Peter Parker's story on his family, on the ghost of Uncle Ben, and away from Iron Man. Tony was never a good role model for Parker, even if he was a protector to him. He used him in Civil War, sought to control him through his technological "improvements" and ended up haunting him in a way that disrespected Ben's memory. In the interest of making Spider-Man Iron Man's replacement, the MCU unwittingly made Tony Stark Uncle Ben's replacement and robbed the heart of Peter Parker's story. Recentering him in Spider-Man 3 through the threat to his family can remind Peter of who is as a hero in his own right, helping him get over Tony Stark - and crucially also step out of Iron Man's reductive shadow - and to honor the memory of Uncle Ben in a way the MCU Spider-Man franchise has so far failed to do.