I have not read through this entire thread yet (but I will after this post) but as for my initial response to
@JTB123 's OP:
I play about 75-80% hellfire. Even in the matchups that really are more favorable to play ninjutsu I tend to stick with hellfire because I want to see what I can learn about every matchup with HF because that is my favorite variation to play, so my response could be slightly skewed by the fact that most of my matchup experience is using hellfire but I will try to look at this from a HF/Ninj combined perspective since the thread is about Scorpion as a whole.
There are several matchups that come to mind that I am fairly sure that Scorpion does lose. Those characters in my personal opinion from playing my friends and others online are as follows: Takeda, Johnny Cage, Dvorah, Alien, Cassie.
There are a few that I think Scorpion "possibly" loses slightly to and those are: Sub Zero (GM is the only thing I am basing this on since it is essentially the only variation that is used), Liu Kang, Sonya.
I really don't believe I am saying this but the only matchups that I feel fairly certain that Scorpion actually wins are: Goro. That is literally the only one that I feel pretty confident that Scorpion definitely "Wins" 6-4.
I feel like Scorpion pretty much goes 5-5 with the rest of the cast. Scorpion is one of those characters where if you are playing against a good player regardless of their character the likely outcome is that the better player will come out on top. With the exception of the five characters that I listed above that I feel he almost certainly loses to, you could really make the argument that he goes 5-5 with literally every other character (assuming the best possible variation matchup for each character). You are not going to see many situations where you have literally no chance to win with scorp but in the same vein, you will also likely not be in many situations where your tools give you a big advantage where you don't have to be as "on point" so to speak.
Ninjutsu has his range, armor breaking, footsies, oki and lack of stamina reliance. Hellfire has his punishment, damage, fbrc mixups/pressure and flame aura/hellfire specials which do help greatly in certain matchups. Both characters lack something very critical to be able to deal with the best pressure characters in the game and that is a good standing armor move. In the context of this game and the risk/reward it brings to the table, EX takedown is simply not good enough of an armor move to demand enough respect. If you are trying to armor out of pressure and your are right, you get 15%. If you are wrong, you eat 30-40%. That is not a good trade no matter how you look at it.
I am certainly not set in stone on my opinions on any matchups and am open to reasons why I may be wrong about this but I really just don't think that Scorpion "beats" (6-4 or better) really anyone other than probably Goro. Scorp is "Mr. 5-5" in my opinion and I don't think that means he is weak or non-viable, it just means you are going to have to be on point with your matchup knowledge, punishes and reactions as well as your spacing and mixups if you want to be successful with him. You wont get many "freebies" in competitive/tournament play with this character but you pretty much have the potential to beat any opponent as well.
That is my thoughts on this.