A key Thor villain in the MCU was changed to the point of being unrecognizable - all because of his similarities to Loki. 2013's Thor: The Dark World is considered a lackluster film in the Marvel Cinematic Universe for multiple reasons, but audiences cited the boring, bland villain Malekith as a prime reason why the film failed to impress. In the comics, Malekith is quite different...but unfortunately, Marvel Studios believed that comic-accuracy would confuse audiences.
In Thor: The Dark World, Malekith is the leader of the Dark Elves and the ruler of their realm, Svartalfheim. Seeking to reestablish the darkness of the universe before the Creation (and wanting revenge against Odin and the Asgardians for defeating him in a previous war), he desires the Aether - which is later revealed to be the Reality Stone, one of the six Infinity Stones. Malekith seeks to unleash the Aether during the universe-spanning event known as the Convergence, thus covering all Nine Realms in darkness, but is stopped by Thor and his allies.
Many fans considered Malekith's motivations to be entirely unrelatable, his powers nondescript and his appearance bland and uninteresting. All these problems are nonexistent in the comics, where Malekith is known for his unique appearance: blue skin with a half-blue, half-black face. Unfortunately, Loki in the film is half-Frost Giant, and has naturally blue skin. Since the MCU was still in its infancy, it's understandable that Marvel Studios feared audiences would think Malekith was actually a Frost Giant and not a Dark Elf, so his skin color was changed.
Malekith is linked to Loki in more ways than his physical appearance. In the comics, Malekith's father and many brothers died in a war with the Trolls, and his mother subsequently sold him for food. He was later raised by a wizard who taught him to become a skilled sorcerer; Malekith later killed the wizard for having the temerity to seek a peaceful resolution to the ongoing war (which Malekith believed would invalidate all the sacrifices his people made to win the war). The wizard scarred half of his student's face black before succumbing to his wounds. Thus, Malekith was abandoned by his family, taken in by a powerful magic-user and taught to use magic himself - a backstory that sounds awfully similar to Loki.
While the MCU has many memorable villains, it is no stretch to say that Malekith is not one of them. The comics version of the character has a tragic backstory that was forged in war, and would have been interesting to see on the big screen. But other, more interesting Thor villains would follow in Malekith's wake, and Loki was allowed to remain unique in his skin color (at least, until Nebula arrived).