Why I don't think that a Scorpion Vs. Noob plot should be done;
1. Scorpion killed Sub-Zero and got his revenge; it's done.
2. In Ashrah's ending, Noob Saibot's stated as "desiring to remain [in the Netherealm]", so I don't think he cares that Scorpion killed him, and may, in fact, actually be glad he did die.
3. They were both generals in Shinnok's army, so technically they've worked together in MK4/G, so it would be kind of weird to have them turn on each other after working on the same side, then go back to how things were before they died, and after Scorpion died.
Their stories are evolving in two completely different directions, they don't need to fight anymore, and it's over.
Edit: Oh yeah, YourSoulIsMine, stick with one account.

They may have worked for Shinnok and Quan Chi back in MK4/MKG, but who knows if they even came across one another during that time?

I think why the Scorpion/Noob Saibot thing should be done is to bring back something to Scorpion's character. Basically, Scorpion would feel some responsibility as he had a part in creating Noob Saibot. I think that also, it would sicken Scorpion that Noob had been serving a bastard like Quan Chi. In addition, Noob Saibot, although desiring to stay in the Netherrealm, might thirst for more power and might become a threat to other realms.

Unitl MK:D, Scorpion's always looked out for himself (assuming his protecting of the younger Sub-Zero was 100% retconned), so I can't picture him caring that much about Noob Saibot becoming a threat to the realms; unless Noob would start something directly with Scorpion, I can't see Scorpion being provoked, especially now, since he's serving the Elder Gods. Although he did create Noob Saibot, Noob made Scorpion; it's an eye-for-an-eye.

We'll see what happens in Armageddon. Also, it does not say anywhere that Noob Saibot ever worked directly for Quan Chi. He only worked for Shinnok. Remember that Noob Saibot received orders from Shinnok alone since MK2/UMK3...

I would develop a special connection between the two. I think that since Noob Saibot's birth in the Netherealm he has long forgotten his past and that he was once Sub-Zero. I think that when Noob Saibot crosses paths with Scorpion it will spark some memory in him. Noob Saibot would be confused with these mixed memorys and thoughts and when he encounters his younger brother and is revealed who he once was, Noob Saibot would have his memory returned to him from his former life.

It was stated in Mythologies that Quan Chi ran the Brotherhood of the Shadow. That kind of denotes he also gave Noob his orders.

I understand why many some don't want Noob Saibot and Scorpion facing one another because it could be really shitty if handled wrong. No one wants to see Scorpion simply go "Grrrr, I still hate you for killing me! Die again!" and Noob to go "You killed me, now I hate you! Grrrr!"

However, I think if it was handled correctly it could be really cool and be fitting.

I think, firstly, Noob Saibot should be the one to make the first move...forcing Scorpion to respond. I think they did run into each other during MK4 or even before....but remember, until Deception, Noob's had no free will. He was Shinnok and Quan Chi's slave. After they were defeated, he immediatly went to Shao Kahn. He even says in his Deception bio, only after his masters were gone was he able to think for himself again. If he beared a grudge or anything, he wouldn't have been able to do anything about it.

However, I don't think Noob does feel a grudge against Scorpion. Since he is proud of what he is, he might even feel a little grateful. I think what should happen in Armageddon is Noob Saibot offers to let Scorpion join him. Knowing Scorpion's power....and Scorpion being Champion of the Elder Gods....he could be a great asset to Noob's power. Giving Scorpion the whole "We are the same. We should be working together." routine.

Or he could simply want Scorpion dead. Not really out of revenge, but because he could see Scorpion as a potential threat....being the man who killed him. Scorpion could find himself a target along with Sub-Zero and possibly Sareena.

I think it would be cool for Scorpion, upon learning on Noob's true identity, was forced to reflect on the consequences of his actions. Perhaps a little tempted to join Noob, but realizing that his blind, selfish revenge created an great evil, and just disgusted with what his former rival had allowed himself to become, he'd concentrate on destroying Noob Saibot.
(I'm referring to pre-retcon Scorpion of course. Post-retcon Scorpion is a retard and probably wouldn't care or simply try to kill Noob for killing him first)

I would like Scorpion and Noob Saibot to have a confrontation because they are two sides of the same coin...which in my opinion makes for a better rivals. Better than Scorpion vs. Sub-Zero.
Both were manipulated by Quan Chi and killed. Both were used as his servants or weapons. But while Scorpion retained his free will and struggled to hold onto his honor, Noob Saibot lost his and became a pure evil wraith. Everything Scorpion does is for his family, but as seen in Deception, Noob no longer cares about his family.
The original Sub-Zero created Scorpion. Scorpion created Noob Saibot.

And finally, I think it'd create a nice sense of coming full circle. If in the end, it came back down to Scorpion and the original Sub-Zero.

*claps hands* Bravo! I couldn't have said it better myself. Not only does it provide for a good ending to that whole story, but also, it would help give Scorpion's storyline some redemption.