From the beginning of Mobile Suit Gundam as a franchise, all their worlds has constantly had characters who aren't entirely good or evil. There's plenty of characters on both sides of a war that can be sympathized with, even if their goal isn't something that people agree with.
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But some Gundam series try to do something a bit different from what's expected. Sometimes it's intentional, sometimes they write characters they intend for viewers to root for that are actually terrible people and would be villains in most stories.
10 Flit Asuno
This isn’t even technically the bad guys. Flit Asuno lost the woman he loved in a war against his greatest enemies, and couldn’t get over it. The older he got, the more grizzled and twisted he became. By the third generation, he was literally just the antagonist, having let the hatred twist his heart after decades of being in battle. It made him into a terrible father, and spent far too much time trying to wipe out the foes of AGE even once learning they weren’t bad people.
9 Char Aznable
Char started out as a villain, the Red Comet who tore apart Amuro’s life and proved the primary threat to Amuro’s life in the series. But eventually, he came around and worked with the heroes as Quattro, fighting against the corrupt Earth Federation. However, he was never really “good”, he was just proven right briefly. By Char’s Counterattack, he was the villain again, unable to tolerate the Earth Federation even when they’d cleaned their act up.
8 Setsuna F. Seiei
Setsuna began life as a child soldier fighting for Ali-al Saachez. He followed those orders until he’d nearly died, allowing it to completely change who he was as a person for a while.
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Having said that, he isn’t exactly a better person after joining Celestial Being. Let’s understand one thing: Celestial Being’s solution to battle is to kill soldiers until the countries give up trying to fight. So they stopped war by decimating so many countries’ powers until nothing was left.
7 Io Fleming
Io Fleming is a cocky guy who grew up in a rich family, even if he wasn’t really a fan of them. He’s the protagonist of Gundam Thunderbolt, but there’s not much likable about him in his introduction. He’s incredibly talented, but in combat he seems more like a sociopath. The Zeon side of things is the likable group for once, even though their methods are still terrible. Although, like similar protagonists Lelouche Vi Britannia from Code Geass and Light Yagami for Death Note, fans can't help but love a sociopathic protagonist.
6 Tatsuya Yuuki
Tatsuya Yuuki was mostly a good guy throughout Gundam Build Fighters. He was a decent dude that held the title of Meijin, signifying he was one of the strongest pilots in their universe, and generally just made friends with the main characters and helped them along their way. But when it came time to face the protagonists, he was forcibly mind-controlled into fighting dirty, and became a literal villain they had to overcome to go further.
5 Chang Wufei
Wu-Fei was a complete jerk who spent most of the series either being sexist, or getting beaten by his rival. One of the protagonists of Gundam Wing, he spends most of the series trying to make up for having lost his wife, who died trying to protect the colony. Trying to figure out his own path, he seems like a good guy because he won’t fight the “weak”, but the actions of their group weren’t ever anything more than terrorism in the first place.
4 Bernard Wiseman
Bernie was recruited by the Zeon early on, and found himself assigned to try and destroy the Gundam Alex in the space colony of Libot.
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However, while he’s there he becomes friends with two characters—a young boy and the test pilot of the Alex. He’s made more relatable than most members of the Zeon, but he’s still very much loyal to his people and risks his life to try and take the Alex out. So perhaps he's not the hero that the members of Zeon believe him to be.
3 Aina Sahalin
Aina is the test pilot for the Apsalus, and gets pulled into the events of Gundam 08th MS Team thanks to her brother and their family friend. Over the series, we see her come in contact with Shiro Amada, the protagonist of the show and the man she eventually falls in love with. The two of them eventually run off together, but up until that point she’s very much on the side of the Zeon, a group that wants to enforce their own unique form of government upon the people and don’t care who they harm.
2 Heero Yuy
Don’t get it twisted. Heero Yuy is a bad guy. People like him because he’s hyper-competent, but he spends his time in Gundam Wing saying he’s going to kill everyone he meets. And even outside of that, one of his most pivotal moments in the series is killing the pacifists in the series. Even though it’s a set-up by the leader of OZ, Heero is technically the reason OZ can declare war on the colonies in the first place. Much of the remainder of the series is about shutting down the conflict he caused then.
1 Build Divers
This group looks cute, right? Well, they’re not. Their best friend is a glitch in the system of the Divers program. Her very existence is risking their virtual realm. It would have been easiest to simply allow the program to be updated and get rid of all of them. But instead, Build Divers fights against an entire army to help her stay. It’s a valiant effort, but at the same time some of the people there can only be their true selves within the world.