Fujin IS the protector of Earthrealm in Deadly Alliance.

But MKDA is set in OUTWORLD. That's why Raiden leads the good guys. Because this time, he wants to go after them BEFORE they attack Earth instead of waiting until their army is at full strength.

So Fujin stays at home and does his job of guarding Earth.

Fujin totally should've been in Deception though. You'd think hearing that Raiden's mission failed and he died would totally motivate him into action. Rumor has it that Fujin and Kintaro were actually both supposed to be in MKD but they went with Kahn and Goro instead.

No. Whats done is done. And ultimately the events of MK4-MKA aren't relevant anymore because of MK9.

I was always under the impression that since Raiden died in Outworld and the whole game took place in Outworld that he just didn't know about Raiden and everyone else failing... Considering nobody goes back to Earth that knows about their unsuccessful mission, it's not implausible.
Yes, we could assume that Raiden could've told Fujin, "If I'm not back in a week, wreck some shit for me," or something, but given how good Raiden's ideas have been since Deadly Alliance, and the fact that his ending in DA says he doesn't have foresight anymore, I can't help but think that he's just a terrible planner for important tasks, like saving the world.

Raiden's resurrection took place in Earthrealm.

And in Armageddon, Fujin knew more about what had happened to Raiden than anyone else did.
Aaanyway, to answer the actual question, here's the things in DA and Deception's story that I would change:
1) Shao Kahn and Goro do not come back from the dead (at least not until Armageddon). Stryker, Fujin, and Kintaro are added to Deception's cast instead. (Story: Fujin's is obvious. Kintaro believes Goro's death was a sign the Shokan were on the wrong side and making peace with Edenians and Centaurs was weakness, he wants the Shokan to fight for warlords and conquerers again, siding with Onaga. Stryker's on the trail of the Black Dragon after his former ally Kabal freed the fugitive Kobra from NYPD custody. Fujin helps by sending him to Orderrealm since Kabal is allied with Chaosrealm.) Also, Zombie Liu Kang would not be a character until Armageddon. Liu Kang's ghost still appears in endings, but no playability.
3) Johnny, Sonya, Jax, Kung Lao, and Kitana were not killed, only knocked out. Onaga does not possess the power of resurrection, just mind control.
4) Dairou is hired to guard Shang's palace in MKDA. He, not Mavado, is the one who attacks Kenshi (this feud carries into MKD where Hotaru is after Sub, Kenshi is travelling with Sub, and Dairou is after Hotaru, so Kenshi and Dairou will meet again in a sort of three-way confrontation).
5) Darrius is a member of the Red Dragon. He's still formed a rebellion in Seido, but his purpose in doing so is to destabilize its government so the Red Dragon can later conquer the place.
6) Li Mei's MKD ending is made canon. Just the part about the mummy in her soul making her join Onaga, not the part about them winning.
7) Konquest is rewritten to make more fucking sense. Specifically the part where Hotaru puts him in jail is moved to take place during MK1 thru 4 instead of him spending "years" growing old in prison between MKDA and MKD, which is impossible because they were back-to-back and didn't take that long.
I'd leave the rest pretty much the same.

Why not just rewrite Armageddon?

Keep Bi Han(MK1 sub zero) dead; Incorpate some elements Of MKConquest into Noob Saibot's back story.

I don't want to see MKD and MKDA rewritten. I love those games (was a bit less keen on MKA). Then it took me a while to get to grips with the current return to 2D. I get why its been done and the new game is great and all but what made the PS2 era amazing (at least at the start) was the bravery to kill main characters, introduce new ones, take big leaps with the story.

I want the next MK game to not even touch the PS2 era, but to go off in a totally different direction. An opening movie I'd love to see is Shinnok getting beaten by Raiden before the game even starts, sidestep the whole MK4 plot (maybe not even have Shinnok in the game itself), this change to what happened in the original timeline allowing some brand new antagonist to step forward.

I thought a missed opportunity in MKD (my favourite MK game) was not having the characters beaten in MKDA available to play as evil brainwashed minions of Onaga. I'd like to see zombie versions of those killed in the latest game back in the next one on the side of evil and some brand new heroes step up to the challenge.

(I do want to see the return of Bo Rai Cho though. And Havik)

My version:

Shujinko never existed. The end.

I really like this idea. I thought Darrius`s character development in Deception was really weak. If we could've eventually found out that he was actually a spy of some sort from the Red Dragon then that would've really been a unique twist as a backround story for him. Darrius kind of already looks like what a soldier/member of the Red Dragon would look like anyway imo..

“Those were $500 sunglasses Asshole.”

If you look in the Krypt, you can see art of Darrius's primary costume with the RD logo on his chest that says he was originally intended to be a Red Dragon member, to replace Mavado and go along with that artifact chamber stage with all the orange glass.