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These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Mileena, who is regarded as the most iconic villainess of the series.
Baraka. The creators have admitted in one of their videos that Baraka is one of their most popular characters, albeit not having been in a lot of the games. Case in point: his inclusion in the DC crossover.
Game Breaker: Kitana's fan lift/pummeling combo, a nigh-indefensible move so widely abused that it was nerfed by a software update that made it difficult to corner an opponent. Some players found a workaround anyway.
Harsher in Hindsight: The special intro in the Super Nintendo port, which features Shao Kahn and Kintaro, is no longer funny now that Acclaim, the company that distributed the first two games in said console, bankrupted. See it yourself here.
It's Hard, so It Sucks: A major issue with the game is it's cheating AI, causing the game to become absurdly hard. It's difficult to enjoy a game when you get thrown almost every five seconds while your attacks are almost always blocked.
Reptile is working his way up. Like Sub-Zero's case with Sareena, the closest Reptile has to a canon love interest is Khameleon due to her hopes to repopulate their dying race, but it's not uncommon to see fans pair up Reptile with Mileena or Nitara as well.
Polished Port: Unbelievably, the Game Boy version turned out really well. Yes, the character roster had to be cut down due to hardware limitations, but the graphics and music are very good, the controls are perfect, and the gameplay is actually faster than the other versions.
Porting Disaster: The Midway Arcade Treasures 2 version had the start button exclusively function as the pause button. This made unlocking Smoke impossible.
Kitana has a history of being repeatedly deceived and/or manipulated by several villains throughout the series. She, during Mortal Kombat 2, falsely believes Shao Kahn to be her father. In Deception, she is under the control of Onaga; and in Mortal Kombat vs. DC Universe, she's being manipulated by both the rage sent by Dark Kahn, and then by Quan Chi. It hardly seems to affect her though. She breaks in her Unchained ending, though, after Blaze tells her that her premonitions were true and Armageddon is coming.
Smoke's misfortunes also seem to pile up with each sequel. To date, he's been converted to a cyborg against his will, deactivated and hung as a trophy after Mortal Kombat 3, and reprogrammed as an evil minion in Deception. Smoke: one way or another, his life sucks.