There’s a real seduction to multiverse stories. Seeing how all the same pieces rearrange themselves into a recognizable but different whole; seeing who these characters really are by removing the trappings; watching how a tiny choice made in a tiny moment causes massive ripples throughout time…alternate universe stories can give us a momentary feeling of transcendence, because in them we see more than a mortal usually can.
In a way, all fiction is a tangled web of interconnected alternate universe stories. Lord of the Rings imagines a new prehistory of magic, monsters, and miracle for our world; Toy Story presupposes an alternate universe in which toys can talk and feel; even the mainline MCU is an alternate version of our universe in which superheroes (and supervillains) exist. Seeing characters we recognize, either by name or by archetype, doing exciting things that we can relate to is at the core of good storytelling.
But in 2021, after thirteen years of continuity, the MCU is finally big enough that it can hold up the weight of its own alternate universe stories.  We know the characters well enough that the archetypes and personalities can be shaken around and laid out in a different order while still focusing our attention on the core of the stories they’re trying to tell.  In a world of shared universes, the MCU is finally daring to be a multiverse.  Loki, like Into the Spider-Verse before it, have dabbled in the multiverse, but What If… is jumping in headfirst.
So what does Captain Carter’s universe have that the MCU we’re familiar with doesn’t?
Spoiler Alert: Plot and ending spoilers for season 1, episode 1 of Marvel’s What If… follow.
In the first episode, Peggy’s decision to stay in the room with Steve causes huge changes to the timeline, but it’s abundantly clear that the personalities of each character are the same; Steve is still self-sacrificial and courageous, Peggy is still caring and willing to boldly act against orders to do what’s right (and Colonel Flynn is still a misogynist blowhard).
When you place the same personalities in a different situation, though, you get an entirely new history.  Put simply, in Captain Carter’s universe, the room of power has a woman in it.  In her male-dominated world, Peggy Carter was, as Flynn angrily shouts to her, “lucky to be in the room,” but What If… presupposes that this was not luck.  It was a choice.  Writer A.C. Bradley makes this idea explicit in an interview with Kakuchopurei:

I wanted to tell the story about a woman who stays in the room. What happens when a woman stays in the room? Well, the world changes. What happens when Peggy Carter shows her worth?

It’s disappointing how persistently disdainful Flynn is of Carter’s presence in the room; even after she’s proven herself many times over by saving the experiment, retrieving the Tesseract, and going on many successful missions with the Howling Commandos and the “Hydra Stomper,” Flynn is still dismissive of her emotional reaction to the apparent loss of Steve Rogers.
But his reaction is more than realistic for the time.  And much like the personalities of characters in an alternate universe remain the same, unfortunately, so too Flynn’s reaction feels unchanged (or not changed enough) in our time as well.  Society wants women and people of color to be exceptional in their field just to be accepted or treated as worthy; and when they are, they’re used transactionally for what they can offer and tossed aside when they’re no longer valuable for that purpose.
And while a disappointing number of people in the Church have looked askance at Captain Carter, the words of Christ are clear: women, you are welcome in the room.
Jesus was a counter-cultural revolutionary in many ways for his time, but perhaps none more clearly than in his care for women. In a time that treated women as property for a man to exploit, He treated them as people and taught them as such.
His genealogy included women in a time where such a thing would be more than a little bit unusual.  His earthly ministry included teachings for women that freed them from oppression, miracles for women including women considered “unclean,” and the presence of women in key roles.  He showed them compassion, even when they did things that shocked the men around them.  And His resurrection was first attested to, in defiance of legal convention and the way stories were typically told in that time, by women.  Jesus’ cultural revolution was centered on the shocking idea that people are all made in the image of God, and his ministry was built on the reality that we all have something to offer.
And after His ascension, Jesus welcomed them to the room, equipped them with the Holy Spirit at Pentecost, and sent them out from the room on His mission.
Flynn insists that Carter is lucky to be in the room.  But in this universe, as in hers, I think he’s wrong.
When women are in the room, the whole world is lucky.