Human Twilight in My Little Pony: Equestria Girls Friendship Games is motivated by a desire to understand the magic that emerges from Canterlot High School. At first, she's blackmailed into participating in the Friendship Games by Principal Cinch, but Twilight's own desires still keep her going even when her amulet starts stealing magic and opening rifts in reality. At the movie's climax, she unleashes the stolen magic and transforms into Midnight Sparkle, getting Drunk on the Dark Side and almost destroying the world.
In Disney's Treasure Planet, John Silver is supposed to be the bad guy; and he does it pretty well, most of the time. But he also turns out to be a great father figure to Jim Hawkins and his soft spot for the lad pushes him to do the right thing now and then. His core motivation of wanting to get what is, in his eyes, rightfully owed to him, is more complex than just standard pirate-related greed.
King Haggard of The Last Unicorn, as shown in the scene where he explains why he captured the Unicorns. Not from greed, or power... but because they're the only things that makes him happy.
Rameses in The Prince of Egypt (yes, the Pharaoh). Unlike the Pharaoh of The Bible, he's shown to be a well-meaning man who genuinely loves his brother Moses and is struggling with his father's shadow, but because of his upbringing, he's blind to certain things in life, like the suffering of the slaves. Yet he's not villainous at all until Moses starts demanding that he let his people go. The writers deliberately humanized him, but made him so sympathetic and tragic that, at some points, they had to rewrite some scenes between him and Moses because Moses came off as being cruel to him. And even then, he still is a very tragic figure.
Aladdin's father in Aladdin and the King of Thieves. As implied by the title, he is the leader of the forty thieves. However, it's implied that his only motivation for wanting to lead them, as well as stealing various treasures, and why he left the family to lead them, was to allow his family to not be impoverished anymore. He also intended to return to his family once he had amassed enough wealth, but by the time he returned, he was unable to find them, and thus he believed they had died.
Princess in the sequel A Howl-iday Adventure also fills this role, greatly contrasting her father King who serves as the film's Big Bad. She's his Dragon but is motivated by loyalty to her father, not the collective Social Darwinist views of King and his pack. There's also how she cares for Runt while he's their hostage, not considering him weak and worthless like the other Rogues.
The Once-ler in the 2012 adaptation of The Lorax is quite friendly and sympathetic for most of the movie, despite being the nemesis of the title character. He eventually makes a FaceHeel Turn partially due to the influence of his family and becomes a rapacious, amoral Corrupt Corporate Executive, and then he has a severe My God, What Have I Done? moment after it's too late and spends the rest of his life as a guilt-wracked hermit.
Xibalba from The Book of Life is a Type 2. He only wants to rule his wife's world out of loneliness as his land of the dead is full of the souls of the dead who's family had forgotten about and/or no longer venerate on Dia de los Muertos and the land itself is full of smoke and dust and none of the life and joy of his wife's world.
In The LEGO Movie, the Big Badis an ordinary guy who just wants to keep his LEGO models organised, although he has a rather Jerkass way of going about it.
In Home, the Gorg may have destroyed the Boov's original home planet, but his children were stolen from him. It's not entirely hard to see why hed be so upset.
Megamind has, well, Megamind as this. Metro City (or to him, Metrocity) has treated him like he's an Evil Genius who needs to be stopped, even when he was a child. The truth is that he isn't and was never evil. When he was a kid, all he was trying to do was make friends and impress them with his inventions, which horribly backfired on him. Once he defeats his longtime foe, Metro Man, he decides that he's done being the bad guy. That is if you don't count him giving Hal powers and said character turning into a real villain.
Huaxian in Little Door Gods gets a neat inversion of the usual hero/villain dynamic in her fight with Yu Lei. She is clearly not especially interested in the goal that the Mayor sets her to, and only follows along because it's a job in an otherwise bad economy. Meanwhile, Yu Lei decides it's a great idea to break the seal she's guarding and suck her into a black hole in the process, all for the greater good. It's also worth noting that at this point in the film it's not entirely certain whether Yu Lei or his idealist brother Shen Tu is in the right, so the audience is justified in rooting for either side. It's a refreshingly serious, well-handled moment in a movie otherwise dominated by fart jokes.
The Cleric from Toy Story That Time Forgot. He lies to all the other Battlesaurs, manipulates them, and tries to destroy Woody and Buzz, all to keep the Battlesaurs from realizing theyre toys. But he only does it because he cares about them; he genuinely believes that they wouldnt be able to handle the truth and that he has to keep them in the dark to save them from a collective nervous breakdown.
Stinky Pete the Prospector from Toy Story 2 also counts as well. His main goal is to travel to Japan to be treasured forever after so many years of receiving no fulfillment. He convinces Woody, Jessie and Bullseye to travel with him in order to make the set complete and to do what is right for them, even if he takes extremes measures such as manipulation and threats in order to do so. Plus, the ending shows that he is capable of redemption once he finally got to be played with by a girl who loves to paint on her dolls.
Gabby Gabby from Toy Story 4 is introduced to Woody and Forky as a fairly unsettling doll with a gang of puppets at her disposal, willing to take what she wants by force (in this case, Woody's functional voice box), and Bo Peep suggests just staying away from her. But as the audience learns from her private time with Forky, she's just really desperate to have an owner, having watched the antique store owner's granddaughter Harmony from afar for who knows how many years. When she has a heart-to-heart with Woody later, he willingly surrenders his box to her, and she sets up a meeting with Harmony... who immediately tosses her aside when offered a home. Gabby tells Woody he can have his box back with no fuss, resigned to her fate as a worthless toy. Thankfully, Woody has other ideas.