Three episodes into the new MCU show She-Hulk: Attorney At Law and there still has not been a character defined as the main villain. The show does focus on several criminal cases, so there are villains in the eyes of the law like the shape-shifting Asgardian Light Elf Runa. But when taking into consideration who the defendant was, the case was one time when it wouldn't have been so bad if the villain won.
There have been a few other occasions in the MCU when the same could be said about other characters seen as villains. Their reasons for receiving the label are usually the deciding factor in whether they win or not, but sometimes the argument can be made that they deserved to get what they were fighting for.
Hela - Thor: Ragnarok
Odin's true firstborn, Hela the Goddess of Death was a villain in Thor: Ragnorok, but she had once been Odin's closest ally in battle as the commander of the Asgard army and his personal executioner. She helped him build Asgard, but when their priorities stopped aligning, Odin banished her and got rid of any evidence of her existence.
After Odin's death, she had every possible claim to the throne. She was Odin's firstborn, she played a crucial role in building the empire, and she had proven that she could protect Asgard against its adversaries. She deserved it, but because of her darker qualities, she was still deemed unworthy.
Karli - The Falcon and the Winter Soldier
Karli Morgenthau in The Falcon and the Winter Soldier was fighting against the injustices that many of the people who survived the blip were facing after they were forced out of their homes just to be placed in communities that were neglected by their governments. It was hard for fans to decide if she was an MCU villain they loved or hated.
Before Bucky and Sam intervened, she was able to disrupt governments and provide resources to many of the displaced people. Even Sam recognized the value of the work she was doing, he just didn't agree with her methods. She didn't deserve to die trying to get back to a unified world where everyone is taken care of.
Nebula - Guardians of the Galaxy Vol. 2
Nebula's journey in the MCU has seen her transition from a villain to a member of the Guardians of the Galaxy. She ran on pure hatred for her sister and the need to prove she was Gamora's equal.
In Guardians of the Galaxy Vol. 2, the sisters finally faced off in combat for the first time since the Battle of Xandar. The Nebula from the first Guardians movie who was fighting for other Guardians of the Galaxy villains did not deserve to win, but the one in Vol. 2 definitely did, not only to prove her worthiness to herself but to also show Gamora how her need to always be better made her sister an enemy. Thankfully it played out this way, giving the former villain her well-deserved win.
Najma - Ms. Marvel
After being exiled to Earth, all Najma wanted for the Clandestines was to make it back home, and to do that, she needed Kamala Khan and the bangle that she wore. Kamala showed hesitation in helping them when she found out just how big of a risk it could be, and Najma didn't take that well.
Since Kamala is Ms. Marvel's title character, Najma is seen as a villain for wanting to proceed with her own mission by any means necessary. While the Clandestines have a cloudy history, in the show they're presented as mysterious and powerful beings just searching for a way home, and they deserved that opportunity.
Zemo - The Falcon and the Winter Soldier
Zemo continued his vendetta against enhanced individuals in The Falcon and the Winter Soldier. Sam and Bucky broke him out of prison so that he could help them track down the Flag Smashers, but he decided to go a step further and get rid of any remaining super soldier serum so no one else could take it.
The serum had been used to turn people into government-owned weapons who in his eyes, lacked consideration for the innocent lives lost during their battles. After the way he lost his family, the endless research that followed, and successfully opening the Avengers' eyes to just how careless they had been, he at the very least deserved to see the serum eradicated
Laufey - Thor
Laufey was the King of the Frost Giants that appeared in Thor. Odin and Laufey had a history as adversaries that started long before Thor. The peace between the two was fragile, so when the young and immature Thor went to Jotunheim to fight the "villains," he reignited the feud.
This made it easy for Loki to lure Laufey to Asgard by offering a way to kill Odin, only for the trickster to betray and kill him. The Frost Giant deserved to see his revenge play out after the Asgardian royals constantly disrespected his kingdom, his people, and his traditions. He did what any king (including Odin) would have done.
Ayesha - The Guardians of the Galaxy Vol. 2
The High Priestess of the Sovereign, Ayesha, was seen as a villain when she sent her fleet after the Guardians in Guardians of the Galaxy Vol.2, but her villainous decision was totally justified. She had hired the Guardians to protect her Anulax Batteries only for Rocket to steal them for himself.
Like any ruler would, she sent her fleet after them to retrieve the batteries only to have them destroyed by Ego, twice. The second time was just a consequence of the Guardians saving the galaxy, but the first time, she should have won. The batteries were hers and after upholding her end of the bargain, she should have been able to walk away from the deal without being robbed.
Killmonger - Black Panther
Whether it had been T'Challa or Killmonger on the Wakandan throne at the end of Black Panther, there would have been a well-deserving Wakandan ruling. Killmonger was a villain that did villainous things for a justifiable cause.
After his father, a Wakandan Prince, was killed for trying to give his people outside of Wakanda some of the power that the kingdom possessed, Killmonger dedicated his life to the same mission. Killmonger believed that it was wrong for Wakanda to ignore their people outside the Wakandan bubble. With all the work he put in, the reasoning behind his drive, and the purpose behind his mission to empower his people, he really did deserve the win.
The Celestials - The Eternals
The Celestials were responsible for the Big Bang and in turn are the source for all things in existence. However, they played the villain in The Eternals since for the new Celestial to emerge, the human race would need to be sacrificed.
Some Eternals decided they didn't want to take part, but since they were created by the Celestials for that purpose, Arishem was right to want them to follow through. Eliminating an entire race is harsh, but the human's purpose for existing in Arishem's eyes was always to be a sacrifice for a greater being.
Loki - Thor
It may be an unpopular opinion for the Thor trilogy, but Loki deserved the throne more than Thor did in the beginning. Thor was immature, egotistical, and lacked regard for the impact of his actions during the first Thor. All those elements were blatantly present in his personality, but he was still named the successor to the throne.
Loki tried to keep Thor's actions in line, mastered Asgardian magic, and killed one of Odin's greatest enemies, Laufey the Frost Giant King. Of course, all those decisions were just pieces of his master plan for the throne, but Odin had raised Thor and Loki as brothers only to show favor to Thor because of Loki's true heritage. If Loki had at least been recognized as a possible contender to take the throne as he had been raised to believe he was, so many catastrophic MCU events could have been avoided.