The Avengers is known for proving that the interconnected worlds of the Marvel Cinematic Universe can work together as a cohesive franchise. However, while the film made history upon release, it wasn't revealed until the deleted scenes that the conclusion could've gone very differently for some of the characters, with Maria Hill becoming Director of SHIELD.
The alternate opening and closing, which can be found on Disney+, uses a framing device to introduce Hill, as she is interrogated by the World Security Council. It sets a tone that the Battle of New York carried many losses due to an outrageous idea that Fury believed in: the Avengers. However, that fact is left ambiguous at the time, and Hill's removed and distraught expression transitions into the start of the story.
The alternate ending picks up where the opening leaves off, as the Council snaps Hill back to reality. They try to probe her for more answers on why the Avengers were a mistake, but Hill flips her narrative to say that it was a fortunate mistake. By bringing the Avengers together, the odds were hardly in Fury's favor. With so many personalities clashing, finding common ground would be nearly impossible.
The Council believed it too and even ordered a nuke to strike New York City, which Iron Man promptly used to stop the Chitauri invasion. Before concluding the meeting, Hill brings up the incident with the nuke, which they tried to sweep under the rug, and tells them they recorded their order to bomb the city. The scene then ends with Hill confirming she will be taking Fury's place as Director.
This change in power is similar to what happens in the comics after Fury drops off the grid. When Hill was Director, she was the acting head during events like Civil War and Secret Invasion. Had this change remained in the MCU, the chain of events would've looked radically different. More immediately, the events of Captain America: The Winter Soldier would have also been handled differently.
The Winter Soldier reveals that Hydra was pulling the strings of SHIELD. Hill may have had a suspicion that something wasn't right, but without clearance, it's a theory that is difficult to confirm. However, as Director, she would have the same clearance as Fury, allowing her to dig further. With her in charge and far more suspicious than her boss, Hill could've easily weeded out the Hydra threat and eliminated it.
The alternate opening and ending for The Avengers paint a very different picture of how the MCU could have been structured. In fact, it makes for a great template to explore in an episode of What If...? Hill is a highly skilled and intelligent member of SHIELD and a worthy successor to Fury. While she never took a leadership position in the films, the door is still open,.