Near as I can tell, Fujin was simply doing his duty as Guardian of Earth since MK4.
Raiden wasn't supposed to lead anyone into Outworld in MK:DA...he was breaking the rules there. Fujin, I imagine, stayed behind on Earth as he was supposed to. Deception took place almost entirely in Outworld....none of Fujin's business as Earth's guardian. And then finally, Armageddon comes along and that's when he moves into action.

Tanya has only really ever betrayed just Edenia, and she only did it once. She never betrayed the Deadly Alliance. She didn't betray anyone to serve Onaga and she never even got the chance to betray him (although, judging from her ending, she would have had the right opportunity presented itself).
From what we know about her thus far, she betrayed Edenia because she's a selfish coward seeking power.

Jade isn't Sindel's bodyguard. No more than Kitana or any other Edenian warrior is. Jade's a soldier and if she defends Sindel, it's because that's her duty as a soldier to defend the Queen.

As for their future, who can say? The same questions can be applied to any other character.

I don't see how those are particularly unanswered questions. You answered your questions yourself.

I think the next MK is going to fix the continuity by getting rid of so many characters, and they are to try to give the new story a fresh start. My theory is that in the new game its set up is gong to make the unanswered question inconsequential.

What's the story with Noob Saibot, Sub-Zero & Smoke?

Reptile & continuing his race, what's the conclusion on that?

Will Baraka ever get to kill Mileena off?

Armageddon, story wise, was a huge mistake. To just stand up and shout "DO OVER" after railroading one of the only half decent stories in fighting games is complete B.S.

I would hope that won't happen, and yet...I can see it coming.

I think there are to be unanswered questions in any story in general if there are plans for sequels/prequels already set. Things that are missed from the past can be introduced through cinematics or other characters views and so on. Look at it like this...if you put a puzzle together and misplace a piece there is a chance you will find it...if not than it either has no meaning to you to look for it or it didn't come in the box leaving you wanting to finish it. Worse case scenario you could use your imagination to fill in gaps or just hope the next game will have answers to your questions. I think it is a marketing scheme/ploy to do it on purpose sometimes in movies,books and all other types of story entertainment so why should video games be any different..?
I will say that if all questions get answered,new ones will probably come to exist.

Most of those weren't actually questions at all. Just "this character I like hasn't been in enough games" complaints.

As far as Tanya, it was a little implied in MK4 that the reason she betrayed Edenia was jealousy of Kitana. She had the throne, she had Liu Kang, both of those are things Tanya was trying to take or destroy.

Hopefully if this really is a reboot, they won't even acknowledge any of that stuff because most of the cast and story should be brand new, other than the core themes and characters like Sub Zero and Scorpion.

I think the biggest problem with Mortal Kombat as of late is that most of the characters just aren't very interesting. For instance, I really don't care about any of the new characters from DA or Deception with the exception of Kenshi and Onaga ...... and while Quan Chi , Reiko, Shinnok and Fujin were interesting, Tanya, Jerrik and Kai were extremely boring throw away characters.

They need to ignore the lesser characters, and flesh out the more interesting characters too .... the biggest being Noob Saibot. He has the potential to be the most bad ass bad guy, way more than Scorpion, but they keep making him to generic ... They try to mold him after Scorpion or Sub Zero, where they should take him more towards his grip reaper persona from MK 4, making him scary like a wraith of some kind rather than just a ninja.

Jade and Sindel also have a lot of potential, but again they need to focus more on their personalities, rather than just reusing the same back story over and over. Give them a new agenda you know. Smoke, Reptile, Cyrax and Sektor also have massive potential to be major players in the MK universe, but they just keep getting generic story lines.

Those aren't unanswered questions, though to be fair, I don't even know what to call them.

You can pretty much apply that question ''formula'' to every character. You're just asking ''what now?''. In my opinion an unanswered question would be something like, ''why did Reiko put on Kahn's helmet?'' back after MK4 came out. Now THAT's an unanswered question.