Yeah, I know what you're saying. Retconning his MKA story and having him continue on with him still being the Elder Gods' Champion is what XiahouDun84 did in his story. Paragon and I continued off from Scorpion's MKA story for our MK: Resurrection story. We're focusing his story on him trying to find a way for his soul to rest.

But yeah, since we are going to keep having Scorpion, his story and character should be done well. I've been doing a bit of thinking, and I think that Scorpion's story in the earlier games could have been a lot deeper if certain elements were played in.

When Scorpion died and descended into the Netherrealm, Shinnok and Quan Chi could have made a deal with Scorpion. In exchange for his services as their spy and enforcer, he can be given a new body and will be able to leave the Netherrealm in order to hunt down and kill Sub-Zero. So not only can Scorpion be granted a new body and his revenge, he'd also have to spy for Shinnok and Quan Chi and report to them.

It would also have been good to have Scorpion be dependent on them every time he "dies" and returns to the Netherrealm. That way, there is a consequence for death, even if he's one of the undead. Having him be a spy could have him make use of his knowledge of Ninjutsu while him being an enforcer can make use of his knowledge of Ninpo Taijutsu, Kenjutsu/Tojutsu, Shurikenjutsu, etc.

Granted, I know that Noob Saibot was a spy and enforcer for Shinnok and Quan Chi, but his character could have been used for something else while Scorpion fills in for that role. You could even have Shinnok and Quan Chi make Scorpion do things that he might find to be questionable.

What do you think? Do you think those ideas could have worked well?

I see two immediate problems with it:

First, if Scorpion knows WHY he keeps coming back, it makes the vow to protect Sub-Zero in MK2 and 3 make no sense. He only did that because he didn't understand why he was still a spectre. Getting his revenge was supposed to let him rest in peace, then Sub-Zero somehow returned and he was like "Oh, I guess I didn't finish the job, that explains it", but then he found out it wasn't the same man and GUESSED "Well if revenge didn't get me into Heaven, maybe I should try making up for my sins instead."

Then in MK4, Quan Chi told him "No, you DO have to get your revenge, and you don't have it yet. The Younger Subbie killed your family." And that's when he dropped the vow, attacked Sub-Zero, found out it's actually Quan Chi he has to kill, and here we are now.

The second problem is that he's never gonna be Quan Chi or Shinnok's ally again after MK4, so if he needs their help to leave Hell, then nothing he does in Deadly Alliance works. Scorpion lets his own self out of Hell just by teleporting at LEAST once in that game's storyline.
It only makes sense if being a "spectre" includes the power to come and go as they please until their "mission" (in Scorpion's case, "avenge myself, my family, and my clan") is complete.
Scorpion's deep enough already, he doesn't need "by the way, I was spying for the bad guys the whole time" tacked on, especially since it makes him look more villainous and Scorpion's greatest strength as a character is the fact that despite being a loner and full of rage and a guy who went to Hell when he died, he's often been TRYING to rise above it and become something heroic and get his honor back. Using him as a weapon against the Sub-Zeroes is all the reason Quan Chi and Shinnok needed to make Scorpion into a spectre, anything more would start diluting the concept and would give Quan Chi too much power over Scorp, screwing with their rivalry as I already explained.
Also, frankly, Noob's "I hid in the shadows and did nothing in every single game" act makes no sense if his job was anything other than spy.

Part of the problem with Scorpion, is that he's been in games where there was no point to him being in them.
There was no point to Scorpion being in MK3, but he was retconed into the story for UMK3 and MKT.
He added nothing(but confusing)to MK4.
The only thing that MK4 did for Scorpion was that he found out that Quan Chi was the real killer of his family.

I think that Scorpion needs to lay low for a few game's, but we all know that that won't happen.

Scorpion was crucial to MK4, my friend.

If not for him, Quan Chi would not have been sucked into the Netherealm and thus, removed from the war. Quan Chi and the amulet is the only reason Shinnok posed a threat to the realms. Thus, it's entirely because of Scorpion's actions that Liu Kang was able to win MK4
Not to mention your "the only thing that happened" is the most important thing in Scorpion's life. If he had never found out Quan Chi was the true killer, where would he even be? That's the central motivation of the character, it's pretty goddamn important.
I can think of a few characters who do way less than Scorpion in the plot, but nobody ever complains they're in too many games. Sonya, Reptile, Baraka, Mileena...