Heres a better question...
When has he won a fight in the story?
A lot of other characters haven't won a match in the story mode of either MK9 or MKX, or maybe just won one or two. How many matches Mileena (who was the empress of Outworld at one point), Ermac, Baraka, Rain (a half god and the brother of Taven and Deagon), Sektor (who was the leader of the Lin Kuei at one point) and others have won in the story? Also, Goro and Kintaro, the 2 most powerful Shokans, they lost in a handicap match to Cyber Sub-Zero in MK9. You can't just take the core of the story, especially that not every story is the same canon. For example, the first MK movie is a different canon then the one of the games, just like the Marvel and DC universe have various canons and versions of the stories of their characters, and as such, the stories of all the characters are different then their game counter parts.
And if you wanna compare Reptile to Scorpion and Sub-Zero just because of the whole Shirai Ryu Vs. Lin Kuei thing, Reptile DOES HAVE a legit big section for his race (not clan) of the Saurians/Zatterans, as he still tries to do what he can do resurrect his race. I mean, how many times we have heard of a clan/army/race/gang for any of the other ninjas besides Scorpion and Sub-Zero? Maybe the Black Dragon because Tremor is from there, but we all know that's Kano's part. And yes, Noob Saibot was the original Sub-Zero, but he no longer cares about the Lin Kuei since he became Noob Saibot, in both timelines (MK:SF to MKA and MK9-MKX). Or how about Sektor's Tekunin clan? How much weight that clan got in the story of either timeline or even canon? And Ermac? Yes his body is made of the souls of dead people yet Ermac actually LIKES that he's that way, as we can see in one of his intros in MKX. So where is the weight?
And you know why Reptile's race have a much bigger section then any group for the other ninjas? That's because that Reptile, since he's important outside of the story thanks for being the first ever secret fighter, has appeared in more MK games then almost any other Male, Female or Cyborg Ninja, so both he and his race can get that very same big section.
Aside from Scorpion, Sub-Zero and Kitana, there is no more important Ninja in MK then Reptile, and that says a lot, considering how many ninjas are in the MK universe.
Reptile can easily make it to MK11, and he will still be important as he always was. I think you're just too jealous of other characters others when Reptile actually got more then most other MK characters, both Ninjas and Non-Ninjas.