Shujinko resurrected the Dragon King.

My guess is that Konquest is pretty much a story mode, spanning between the time of MK Mythologies all the way up until MKD.

It's pretty obvious if you ask me. It starts with a young Shujinko setting off on an adventure, then somewhere down the line he meets the elder gods, who set him off on a task o retrieve an item(I forgot the item name, it's in his bio though) but once he finally finds the item, he realizes the elder gods have tricked him(Hence, Deception) into resurrecting the Dragon King(Onaga)

This could also tell why the elder gods don't want to interfere in Deadly Alliance. They know Shujinko is close to the resurrection.

What is their motivation for resurrecting Onaga?

Simple

The elder gods have absolutely no say in what goes on in Earth Realm, but in the other realms that have been manipulated into OutWorld they do have a say in what goes on. More or less, they're power hungry. Shang Tsung, Shao Kahn, and Shinnok have all been unsuccessful in taking Earth Realm, and the only person who can take it is dead.(Onaga) So they get a young, ignorant boy, Shujinko to the dirty work for them.

That's just my guess.