I've pretty much understood the whole time travel thing, but something that I can't understand is how the new organization will reunite again like MX said in the end of DDD?

 

Since they all belong to diferent ages, how will they meet at the same time?

What about Xemnas and Ansem TSoD? From what I know, story cannot be changed, so why are they back since they were destroyed? For Isa and Braig i get it. Their Nobody and Heartless were destroyed, making it possible for their return, but Xemnas and Ansem were destroyed so old MX could return, so how are they back???

Xemnas got revived and the Ansem that's in DDD isn't the real one(I might be wrong) 

I'm sure Flaming Lea can explain this better

 

YX can travel throught the time, so the Ansem SoD and Xemnas you saw at the end of DDD were "older" versions of them. Before they were killed by Sora. YX just traveled back in time and gathered them, and he will do the same in KH3 I think.

Since MX only needs them to forge the X-Blade, I guess they would return to their times after that, so the story isn't changed.

 

(another solution: time travel doesn't make any sense )

Ansem SOD and Xemnas returned thanks to time travel. The ones we see in DDD came from some point in the past before they were destroyed.

They will do what they did before in KH3D. They will all travel through time to where they gathered in KH3D. I believe Vanitas will be the one in the 13th chair instead of Sora.

There isn't a new Organisation XIII. They are the thirteen Seekers of Darkness.