Reptile was a ninja in the 2D games. They changed him to something completely different once they went to 3D. They actually made him look like a lizard. Which I hated, by the way.
Am I the only one that liked how in the 2D games all of the male ninjas, all of the robots, and all of the female ninjas looked alike? I liked that what set them all apart was their abilities, not their looks. Just having a color swapped suit was fine with me.
I say that because many of them transitioned horribly to 3D. Especially Jade. She looked like a man with long hair (or braids in her alternate costume) in Deception. Sonya looked like a man in the 3D games too. Kitana's transition was decent. Mileena had the best transition, because 3D technology allowed her to show off those teeth.
Sektor and Cyrax has okay transitions, but they never looked as cool as their 2D counterparts. They just looked plastic robots instead of metal robots. Smoke's robot look was okay, and I hated his alternate appearance as just a cloudy looking substance. His alternate should have always been his Human Smoke attire in the 3D series.
Like I stated, Reptile's transition wasn't that great. I liked the mask hiding his reptilian features. Just like how Scorpion hides his. I hated both Scorpion and Sub Zero's 3D transitions. I wish they'd have just let them look somewhat alike instead of trying to differ them with completely different costume styles. Noob Saibot made a pretty good transition. He looked as good in Deception as he did in MKT. Rain's transition sucked. He looked really stupid in Armageddon. And the award for my least favorite transition goes to Ermac. I'm sorry, but I hate him in his 3D form. He looked cool as a red color swapped ninja, but his cloth-like attire in the 3D games just weren't doing it for me. I can't comment on Classic Sub Zero since he never appeared again because it turned out he was Noob Saibot.
Anyways, I went way off topic, so I'll just do my favorite's list:
1. Classic Sub Zero
2. Scorpion
3. Reptile
4. Human Smoke
5. Rain
6. Noob Saibot
7. Ermac