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Scorpion (pictured right here) and Sub-Zero are among the most popular characters in the series. At one point, a lot of the newer characters (Smoke, Ermac, Noob Saibot, etc.) were directly based off their character models. In fact, Noob was later revealed to be the original Sub-Zero after the younger Sub-Zero (debuting in II) made his first unmasked appearance in Mortal Kombat 3.
Although he's one of the "ninjas" who was riding off of Scorpion and Sub-Zero's popularity, Reptile has established himself as a lesser darkhorse among the fandom due to being the first Secret Character in the series (which sparked a great amount of interest in discovering and facing him, not unlike Akuma in Super Street Fighter II Turbo). Being an odd anti-villainous example of a Butt Monkey as well as theCosmic Plaything of the series, as well as sporting one of the better fight scenes in the movie has helped to give Reptile something of a cult following among MK fans.
Although his role in the story (Especially after MK9) is a Base Breaker nowadays, Raiden was always one of, if not the most popular non-ninja character from the first game thanks to his Nice Hat and gibberish in his flying move with many finding him fun to play as. Being inspired by Lightning from Big Trouble in Little China (Whose already an ensemble darkhorse) and having a movie performance that is generally considered to be fun to watch also helps him.
Trevor Goddard's performance in the movie as Kano was very well-liked by fans due to it adding a cocky, money-grubbing sleazeball personality to the flat depiction of the games, so much so it was carried over.
Kabal and Ermac were mild Base Breakers at the time of their debut (vanilla MK3 and UMK3 respectively) due to being overpowered. After being toned down in later revisions, they moved over this way and returned for Deception. Rain, originally a goofy Joke Character ninja Palette Swap who doubled as a Shout-Out to Prince and made his debut in UMK3, might also be heading this direction (at the very least, he's out of Base Breaker territory). When it was revealed that he was one of two characters from the original trilogy to not be playable in 9 (the other being Motaro, who actually does cameo in the story a few times), Ed Boon's Twitter was flooded with demands for Rain to be included as DLC. They got their wish.
Also from Mythologies (and probably second only to Quan Chi) is Sareena, a member of Quan Chi's Amazon Brigadewho had a change of heart after Elder Sub-Zero spared her life. For a relatively minor character, she garnered a sizable fanbase and demand for a return. She was finally made playable in Tournament Edition (one of the two portable versions of Deadly Alliance) and Armageddon, where she forms a strong bond with Younger Sub-Zero. Being The Atoner and The Woobie also helps garner endearment points from the fans.
Kenshi from Deadly Alliance (think Daredevil plus telekinesis) is one of the few characters from the post-Trilogy era to earn unanimous praise from the fanbase. How popular is he? Popular enough to make it into Mortal Kombat 9 as DLC despite the roster mainly consisting of characters from the first three games.
Perhaps the greatest example of this trope is Tremor, a member of the Black Dragon clan and the onlyninja to not be playable in the main series. What makes this so exceptional is that he hails what is undoubtedly the worst game in the series by an Outworld mile. Ed Boon himself commented (via Twitter) on Tremor's surprising popularity, calling him "the new Rain." While Tremor wasn't included in 9, Boon has refused to outright say that Tremor will never be included again in the series. Fans, when the inevitable Mortal Kombat 10 is announced, you know what needs to be done.