Well not really screwed up, let me put this story into perspective. This should take place before Mortal Kombat, where Shujinko is training to begin in it.
Alright, you start off in a village, with Shujinko as a young man. He is trained by Bo Rai Cho, of the Order of the Light who will one day also train Liu Kang. Alright, you know about the few adventures, but now you come to Sub-Zero. Obviously this Sub-Zero is mean't to be the Younger Brother, but lets just try to fit this into the timeline: It's the father or grandfather of the Sub-Zeros we know of. It explains why he's wearing the Kori armor, as one of them must of knew of their Kori Ancestors.
Shang Tsung offers you an invitation to the tournament of Mortal Kombat, and you find Kenshi. It was never stated when Kenshi became blind. You find Ashrah, who also really fits into the timeline, as she's a demon that maintains her youthful look by slaughtering evil. This is why she challenges Baraka (his look can be explained, as this may be a different Baraka of the Tarkatans). You also find Ermac, who is weak later on in the story (possibly because he was once good, before Shao Kahn took full control of him). Than you find Scorpion, who is already a Spectre. There really isn't anything wrong with this, besides he wants you to find Quan Chi (he's not suppose to know Quan Chi really killed his family).
You fight Quan Chi, and now here's the real messup: Noob Saibot.
(Here's a side theory. Noob Saibot really has been working for Centuries, but joined his tainted soul with Klassic Sub Zero after he died.)
There's really nothing wrong with the Storyline, once you encounter Havik, Hotaru, and Jade however. You meet Kano and Li Mei later on, which still really has nothing to do to mess up the timeline. Now here's the big part of the explanation. Hotaru takes you to Order Realm, and locks you up for many years. I think time in Order Realm progresses faster than in Earth Realm, so when Shujinko returns, it is around the time of Mortal Kombat Deception, explaining his absents in the past few games...and there you go. Basicly everything else works out.

damn... nice NuB

Quite thurough....but there is still the problem about how Jax, Kabal, Kobra and Sub-Zero's attire that really Break up the continuity.
Jax - He's at the bridge that connects to Liu Kang's training ground. Thr problem here is Jax is a human, and if he was to be there that early on that would make him about 80 years old by the time Shukinko finishes his quest; which at the time he and Sonya were busy with Mavado and the Hsu Hao mess.
Kabal - He's seen very early on in the Chaos Realm when Shujinko is still a young man. Same as Jax, but with even moreso of a problem. If at the time he is seen is still waaay before Liu Kang defeating Goro in Mortal Kombat, then why is he in his breathing aparatus? He wasn't jumped THAT early on.
Kobra - Pure goof here. He's from Earthrealm and he's at the Earthrealm docks from the bigining of Konquest to the end of it. No way can he be that old.
Sub-Zero - Ok this one is just me nit-picking. He doesn't get that armor until after Frost turns on him, so why does he have so early in Konquest? I know it is a bit of a waste to program his fighting model from the older games, but if they had it be pretty cool. Now the reason why you're explination doesn't quite work here is that even though I agree it doesn't have to be the current Sub-Zero, the armor is hidden in a cave in Outworld. It also has to do with his real race, seeing as how he's a kryonic, and not human(which can explain why he may be so old).
But with those said, they really don't bother me much. It doesn't change the fun factor for me at all, and I'm able to over look it.

It's not so much incorrect, so much as it is horribly horribly out of order.
I haven't found any story inconsistancies in Konquest that couldn't be chaulked up to anything more then faulty timing.
So long as you take the order in which events happen with a grain of salt, everything still pretty much works out to be canon.
About the only things that can be taken as correctly ordered are the main quests (And those are still a bit iffy) All the sidequests, though canon as far as happening, are not canon to the times at which they happen, since the player is free to do them whnever he/she wants, thus screwing up what little timeline there was to begin with.
So again, you just have to take things with a grain of salt.
And in regard to Shujinko's ridiculously fast aging, (minor spoilers follow) I chalk it up to the freaky pool in chaosrealm. Up until then not much time passes, (5-6 years, tops, all pre-mk1) so his aging seems normal, but after that, many years pass, but he continuies to age rapidly because of the magic chaos juice infused in him. That's what I theorize anywhoo.

I like both of your views. Like I said before, I thought maybe the Armor Attire, was probably traditional for Sub-Zero's people. Seeing that his father or grandfather could of worn the armor and such. However, on the Kabal and Jax thing, you got me there. As for the aging, like I said before, I belive time progresses faster in Order Realm than in Earth Realm, that is why Shujinko aged in such a short period of time.

What are characters like Kabal and Stryker doing in other realms in the first place?
It's just completely nonsensical. It's also very coincidental. I find it extremely hard to swallow that he JUST HAPPENED to run across all the MK characters in key moments. It's like Forest Gump or something. This hapless moron is just bumbling around and just happens to be everywhere anytime something major goes down.
I don't think we're supposed to take it seriously. I am guessing in future games it's going to be Shujinko went on a massive life-long lasting quest to find the Kamidogu, but all the little details won't be taken as canon.

I think what Nub-Saizero stated is the best way to inturpret the timeline......And I like the whole Forest Gump comparison lol
Though it's a flaw, I think seeing Mokap in the other realms was hilarious, especially if you hit him after you do the side quest for him in the Chaosrealm "Oooh, my balls!"

I just think that Boon made it that way so that you wouldnt have to go through a whole 70 years before meeting the cool guys.
Good going Boon

Konquest is just another crap.... it just wanna show all the mk characters.... bo rai cho trained Shujinko of earthrealm...??? C'mon.... he's from outworld ..... training outworld warriors...... Shujinko supposed to be pre-generation of liu kang... the time before liu kang and the gangs were born..... not next-gen of liu kang....

Way I'm looking at Konquest is the basic gist of the story is canon. Shujinko was decieved into going on this quest across all the realms and along the way may have bumped into SOME of the characters.
But the details, like fighting Noob Saibot in the Chaos Realm, running into so-and-so in Order Realm, Shao Kahn going for a casual stroll through Outworld..etc. should be for the most part ignored.

i agree with Xiaou, but personally i hope the MK krew disregards and basically writes over most of the Deception storyline (much like they did with MK4 and a little bit of DA)... IMO it was crap

Anything you HAVE to do in Konquest in order to further progress in the game is canon.
Everything else is either not canon or speculation. But for sure anything you have to do to go further in the game happened, just at different times. For example, Shujinko meets Scorpion and Quan-Chi when he's and old man, not middle-aged, cause that would make more sense. Just switch up some of the events in time, and I think we got it.

Even just counting the stuff that HAS to happen it's extremely goofy.
He just HAPPENED to run across Scorpion, Baraka, Kenshi, ect. in his travels?
Nightwolf's scared land is.....a small patch of grass just one mile away from the Lin Kuei temple?

Hey, man, it's just a game. Yes, that is how it happened.
Nightwolf's sacred land I'm sure was alot bigger, but hey it's a video game. There's only so much you can put in. Don't take it all LITERALLY.

Why is everybody suddenly taking Noob Saibot's ending as canon? I know it's a great ending but it still is a "what if?" scenario like all endings in Mortal Kombat games.