It sounds like a nice idea, but here are some things to remember.

Firstly, Motaro is dead. Shang Tsung betrayed Kahn and given the Emperor's nature, I am sure he'll be less than forgiving towards Shang Tsung. That being said, Shang Tsung is also dead. Liu Kangs MKD bio tells us this. Resurrection is their only chance at being back I guess.

Onaga does not want Earthrealm. He wants total command over all realms which is why he seeks to fuse the Kamidogou. Unknowingly he'll bring about the end of all realms. He's doing this due to the One Beings manipulation.

Shinnok will not partner with Quan Chi as far as I see it. Chi betrayed and destroyed Shinnok. Quan Chi is also possibly dead and Shinnok may still exist in the Netherealm somewhere. You also forget that Onaga has the amulet now. Scorpion is the Elder gods champion and he has nothing to do with the Netherealm really. Then again, I beleiev they retconned Hell and made it apart of the Netherealm, so I suppose that could be gotten away with. Drahmin and Moloch are both missing in action. Nothing has been mentioned of their whereabouts. They should have been in Moloch's Lair which would mean they'd be trapped under the rubble of the Shang Tsung's Palace which Raiden destroyed in the MKD intro.

Until MK7 arrives, we have no idea what wil have happened to the forces of Earthrealm. Raidens own state of mind hangs in the balance and Onaga still has the 5 main Earth warriors under his control. We'll see then if this part of what you said will come into being. As for Fujin, he's missing and hopefully he will show up in MK7.

I do like the overall idea of having arenas set in all realms. It would make this MK game so much more interesting. We just have to wait and see what happens.

That idea of grouping all of the characters according to their affiliation is a nice idea. It reminds me of that classic title from Playstation called "Bushido Blade 2" it was a neat game that had a great story. As you would choose your character you would enter ten fights and follow the story of that character. Depending on which character you choose would determine which boss you would fight and on top of that, which characters you would fight.

True, but you know how consistent they are with the storyline, TGrant

thats a really cool idea just need to work on the story line abit

I'm thinking something like this:

Shinnok will discover Onaga's plot to combing all the realms and become the One Being. Shinnok will stop Onaga and try to kill him at in attempt to combine all of reality for himself, Shao Kahn then interupts and tries to kill the both of them. The fight is stopped by Raiden and they all hide, and plot an attack. Onaga uses his army and invades earthrealm to house them. Shao Kahn uses his militia and the Tarkata to create an army in outworld. Shinnok returns to the Netherrealm and gathers an army of Onis and appoints Noob Saibot as his general. With Onaga in Earthrealm, and Shao Kahn in Outworld no one is safe. So Fujin (the protector of Earthrealm) gathers the warriors and heads them to Edenia for safe keeping, while he tries to bring Raiden back to his sences to lead the Earthrealm fighters so Fujin can return to Earthrealm. He does and Raiden gathers the Edian army (led by Sindel, Kitana, and Jade), the Earthrealm warriors, and the Shokan to stop Onaga, Shinnok, and Shao Kahn.