Modern fans likely think of Sonya Blade and Kano as irreplaceable in the Mortal Kombat canon. They both date back to the original game and have appeared in many spinoffs, including movies like the upcoming 2021 reboot. Yet both of them vanished in Mortal Kombat 2, only to return in later games. The explanation, simply, is popularity - or at least what limited data seemed to show at the time.
The Mortal Kombat 1 roster was limited to just a handful of fighters. Beyond Sonya and Kano, the lineup of Mortal Kombat characters consisted of Liu Kang, Raiden, Johnny Cage, Scorpion, Kano, and Sub-Zero, with Goro, Shang Tsung, and Reptile also being included as non-playable enemies. Reptile was a secret character with no biography, and most players never saw him until the sequels, since unlocking him required a Double Flawless victory in the Pit and finishing the match with a Fatality - all without blocking and only when a silhouette crossed the moon.
Series co-creator John Tobias noted on Twitter that he and fellow creator Ed Boon added trackers to the first game's character select screen. Using a hidden button sequence, they could discover the most popular fighters on any arcade cabinet, and they did so on machines in the Chicago area. After gathering that limited amount of data, Sonya and Kano were judged unpopular (or rather, unpopular enough) that they could be ditched in Mortal Kombat 2 to make room for newcomers like Baraka and Jax. The overriding issue was storage, which was limited on 1990s arcade hardware.
Why Early Mortal Kombat Games Removed & Reintroduced Certain Characters
Players were more upset by the missing fighters that expected, so they were brought back for Mortal Kombat 3, despite an even bigger set of additions. The same popularity-based triage was still applied post-MK1, specifically to Baraka, Raiden, and Johnny Cage. A full, uncut MK roster only became available in the first direct-to-home game, Mortal Kombat Trilogy, as memory limitations were finally gone.
Mortal Kombat's roster continues to fluctuate, but now more likely because of production and story concerns. Mortal Kombat 11, for instance, lacked characters like Shang Tsung and Mileena in the base game, but they became available in MK11 expansion packs. Presumably, this is because the sheer amount of art, animation, and balancing involved in creating modern fighting game characters made them impractical to include at launch. The internet and DLC have even made it possible to sell characters that have nothing to do with the games' universe, such as John Rambo and The Joker. The next Mortal Kombat game could theoretically have an even more varied roster.
Source: John Tobias/Twitter