Wasn't he wearing a mask?

He was.
People seem to ignore the fact that Reptile was always a Raptor with green scales hidden under his costume. If you don't believe me, perform his Acid Spit in MK2 and UMK3, and perform his Fatalities in UMK3 and the eating one in MK2; you can see clearly that he has reptilian features (the green skin is a freaking give-away). The pink skin on his costume is part of his costume; always has been, always will be.

The real reason reptile wasn't like that was because of arcade ram and they wanted more characters but story wise, Jerrod is right.

Right then these are the flaws and the reasons that mksm sucked.

1)Reptile only served Shao Kahn so that he could have his race resurected. That is also the reason that he protected Shang Tsung.

2)The Scarred Sub Zero if in fact they wanted to put in Sub Zero's brother then that would be following mk3's storyline. And if that was so then why the hell did they make it Kung Lao who cut his eye. I always thought that it was either the mark of excile from the Lin Kui or a scar from a battle with on e of the cyber ninjas.

3)Jade's death is total bull shit. That fucks up mk3, mkd, and mka.

4)Cage kills Goro? WTF!!! Since Kung Lao wanted to avenge his ancestors so bad he should have been the one to kill goro. This really fucked up the rivalry that was between Goro and Kung Lao. As seen in MKG and MK2.

5)Liu Kang is a total dumbass. I have never really liked Liu but he never came off like a dumbass to me I mean he is the mortal kombat champion. Would that not mean that he was at least smart enough to tell when Rayden was being impersonated.

6)Kung Lao got the short end. I always liked kung lao he was and still is my favorite character. But they made him a jackass, self centered, hot head. When in fact it was believed that the only reason that he was competting in the mk tournament was to avenge the death of his ancestor. Other than that he was peaceful and stepped up when Earth Realm was in danger.

7)Sub Zero was awful. They made sub sero suck out them all. His game character sucked both the computer and the playable. All of his moves sucked as the playable one. The slide, the ground freeze, and the fact that you couldn't upgrade his freeze. In Gameplay you only see him for like a grand total of ten minutes.

8)Scorpion had the worst plot turn. Going to the netherrealm sucked period. But when scorpion showed up it just went from bad to worse. He had no point or purpose for showing up. The only reason that he was in there and the same goes for sub zero is that the mk team would not make an mk game without either one of them.

Don't get me wrong I love the idea of an adventure mk game but mksm is just messing with the past and screwing with future games.