I would take the 3D stories - the revival of Onaga and the Dragon King's Army, Shujinko's journey to gather the Kamidogu, and Taven VS Daegon and the Pyramid Of Argus - and mash them together into one concurrent story, that's being told while Taven is helping Shujinko escape Shao Kahn's prison as Armageddon is drawing near.
I'll never understand why Shujinko gets so much flak. He's legitimately the Pai Mei of Mortal Kombat. You sprinkle the two of them (mostly Taven) with some Redesign Cool Dust as we've seen succeed with plenty of other characters (the most recent and amazing of which being Sheeva and Fujin), team them up like a young boi + Granddad version of Liu and Lao, and that's your new Shaolin Monks style team that you could build a whole new game around. A completely reborn rendition of Konquest, in which you could tell ALL the story there is between the Six Realms - the fall of Edenia, the true nature of the One Being, the relationships between the Elder Gods, the war over water between Orderrealm and Chaosrealm, the Outworld rebellions, what life was like when Onaga was in charge, how Shujinko's interactions with other Kombatants over the ages shapes the events of the timelines, and for the love of all the realms, BRING BACK ALL THE MARTIAL ARTS INFLUENCE. One of the BIGGEST reasons I love the 3D games is because they were FULL of the stuff, from the dozens of fighting stances and weapon styles, to the Koncept Art in the Krypts explaining them and showing you the mokap footage of the martial artists. It's one of the things that's made MK great forever, and I would LOVE to see them so back to that well. The material is all there and could easily be shaped into an AMAZING action/adventure experience.