ore probably Shujinko, but we wil never know untill MK7.

Endings are a "what if" situation, for what would happen if that character won. Some can happen even if that fighter doesn't win, for example, Kira's, which doesn't require her to even meet Onaga for it to happen.
Out of the two characters mentioned, and as much as I hate him, all signs point to Shujinko being the man who defeats Onaga. He is built up as the main hero of MKD, and Boon said they intended him to be the next Liu Kang, although fan response to him hasn't been good. Quite a few other characters endings also assume that Shujinko is the one to beat the Dragon King, Raiden's for instance, while nothing backs up Scorpion's ending happening.
Of course, we don't know for sure, and MK has a history of abandoning plotlines and changing events (they did this badly in MKD) to make way for new ideas.

Hmm.. That doesnt make sense becouse the new Mortal Kombat Deception comic book preview insinuates Scorpion to be the one that defeats Onaga.
I think the first few pages of issue #0 shows Scorpion's abilities being enhanced by the Elder Gods becouse he is chosen to be their MK champion. Thats pretty consistant with Scorpion's profile and storyline in the video game but its also conflicting with Shujinko's.
Im thinking the creators had Scorpion also defeating Onaga in the game just in case the Shujinko storyline wasnt well recieved. That might explain why the new comic book is endorsing the Scorpion version.

Speaking of shinjunko... if he defeats onaga, he gets killed by raiden, so he might do it just so the developers don't have to use him in the next game lol

Interesting. I haven't seen the MKD comic yet, so can't comment on that. In the game, yes, Scorpion's powers are e4nhanced by the Elder Gods, but quite a few endings tie in with Shujinko being the one to beat Onaga, plus Midway made the main storyline revolve around him.
I am not sure Midway had any involvement in this comic, or if it's just like the old Malibu comics. If Midway didn't make it, then it shouldn't be seen as canon. If they did, perhaps it's their way of changing events after poor fan response to Shujinko. Does anyone know for sure if Midway are involved in the MKD comic.
I think there is a good chance Shujinko will win, even if, or because most fans haven't liked him. As the guy above me states, Raiden's ending has him kill Shujinko AFTER the move theif defeats Onaga. So this could be Midways easy way of disposing of a poorly received new hero, as Shujinko's role would be done, and it wouldn't damage the flow of the rest of MKD's story. Not that it can really be damaged any more, but still.

it is basically a known faact that ONLY the elder gods champion could defeat onaga..and as we discovered in konquest...scorpion is the champion....
but it could be more....it could be sindel...or tanya....or they could go in a new direction...
but im tellin u..th elder gods champion has a good chance...scorpion 60% chance...others like 30%

Then how do you explain that during Konquest, Shujinko was able to defeat not one, but two of the Elder God's champions. Scorpion himself, and earlier on, Monster. Anybody who can beat the god's chosen champions has a far better shot at taking down Onaga than those beaten champions. Shujinko's ability is that he can absorb other fighters powers and abilities, theirs included.
I despise the character, but I think Shujinko will be the one who beats Onaga, and then, hopefully, Raiden will destroy Shujinko and we can get rid of him. The old fart will have fulfilled his role, so it wouldn't wreck the storyline, and I think most players would rather not see him again.

So, who's the other 10% ?