The Marvel Cinematic Universe isn’t afraid of changing the ground rules when it needs to. Avengers: Age of Ultron, for instance, introduced artificial intelligence as a practical reality in its universe, while Avengers: Endgame’s introduction of time travel led to the multiverse playing out in current and upcoming entries of Phase 4. One place the MCU hasn’t ventured yet is cloning – at least in any significant way – though like so many other ideas, it has plenty of material to work with.
Clones have played a big role in a number of prominent Marvel comics storylines, and while the MCU has no shortage of story options right now, the appearance of clones in the MCU is likely a question of "when" rather than "if." Clones are attractive to comic book creators because they make convenient ways to bring back dead characters, as well as creating natural drama from questions of identity and the soul. Marvel has good and bad clone stories in its history, both of which have the potential to find expression in the MCU.
The best Marvel clone stories often involve the X-Men, whose genetic mutations make them ripe for the kind of evil scientist plots that suit cloning. Mister Sinister became the go-to villain for that, most famously in the creation of Jean Grey’s clone, Madelyne Pryor. More benevolent cloning has occurred as well, notably with X-23 – a clone of Wolverine – and Charles Xavier’s "X" body.
Other properties have not fared as well with the cloning notion, notably Spider-Man, who had a number of significant story arcs built around Peter Parker clones. The first took place in the mid-1970s, following the death of Gwen Stacy. It was eclipsed by the infamous "Spider-Clone" saga from the 1990s that resulted in significant retconning. Mile Morales would then be the focus of an upcoming storyline involving cloning. Whether it's with Spider-Man or the X-Men, these are some future options for the MCU, and that's not including the other cloning endeavors the comics have explored.
The MCU has dabbled with clones here and there in the past. Agents of S.H.I.E.L.D.’s Life Model Decoys are the most prominent example; however, beyond that, examples become thin on the ground. For instance, White Vision constitutes a potential clone already in the MCU, though as an artificial being, he’s less a clone than a mechanical duplicate. Similarly, the two Captain Americas who fought each other in Endgame aren’t clones; they're parallel Captains from alternate timelines, which is similar to how the God of Mischief is returning in Loki, as he is from an alternate timeline, not a clone.
In fact, that may be one of the biggest reasons why a cloning storyline will likely wait with the MCU. The property seems to be focusing heavily on the Multiverse with Loki, What If…? and Doctor Strange in the Multiverse of Madness, which means it can tap the dramatic potential of duplicates without having to create a new and elaborate backstory for a clone. Similarly, Secret Invasion can play heavily with mistaken identities, another common clone trope that the MCU can insert more easily at this point as opposed to using real clones.
There are reasons outside of the MCU canon that could play a part as well. Fox’s X-Men movies made cloning the focus of Logan, which – when combined with that movie's sterling reputation among comic fans – means that the MCU needs to exercise care when approaching similar stories.
Any of those reasons alone may be enough to push cloning out of Phase 4, which lacks the time and reasoning to jump down that particular rabbit hole. That isn’t to say it won’t happen, merely that it could be better developed during a later stage, especially if tied to Spider-Man, the X-Men or another character with clone connections. However, for now, it seems like the MCU will largely leave the clones to Star Wars, though it would be surprising if they kept it that way.