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.
Anticlimax Boss: Shinnok. He just didn't have the fear factor of guys like Shao Kahn or Shang Tsung, and on lower difficulty levels, he doesn't even use his special moveset changes. Especially jarring since he, as a fallen Elder God, he is supposed to be leagues above them both yet comes across as a 2nd-rate Shang Tsung. Even Ed Boon admits that Shinnok probably shouldn't have been the Final Boss of 4.
The fact that he's selectable from the start should be telling, too; it's much easier to face a final boss when you know how he plays. M. Bison at least had the excuse of having been added to the roster in upgrades to his original appearance.
Ensemble Darkhorse: Tanya is the only MK4 character that appeared in a sequel that wasn't Armageddon and she is well liked and was requested many times for DLC for Mortal Kombat 9. She didn't make the cut, but she does make sporadic cameo appearances in Kahn's Coliseum as one of the chained female prisoners (along with Kitana, Kira and Skarlet).
Reiko too. The speculation his ending caused may have had something to do with it.
Narm: Pick an ending from any version and have fun. Jax's ending in particular.
The Game Boy Color version was a cheap and unplayable bastardization because of technical and graphical limitations. With "music" that's a complete nightmare and makes music in pirated bootlegs look good by comparison. Prepare yourself.
Replacement Scrappy: Jarek was hated by fans who felt that he was nothing but a re-hash of Kano's moves. This is because he was originally supposed to be Kano, but the developers wanted more "new" characters, so they reskinned him.
Tanya and Reiko were this, mainly in the eyes of the fans of Kitana and Noob Saibot respectively, because they wanted the latter to appear instead of the former. Surprisingly enough, it didn't last long and got Rescued from the Scrappy Heap, becoming fan favorites because of their distinct personalities (Tanya being a traitor to her own realm and Reiko of an enigmatic enforcer who suddenly puts on Shao Kahn's helmet in his ending).
Tough Act to Follow: Coming up after Ultimate Mortal Kombat 3. This game is supposed to return to its' dark atmosphere and having exclusively two fatalities per character, as well as two stage fatalities. Sadly, this game lacked the charm of the first three games.