As usual, Kingdom Hearts games answer a handful of questions regarding the story and leave much more of them unanswered.
Haven't completed the Final Episode yet but from KH2: FM+ and 358/2 days extra cutscenes it should be obvious what happens.
As soon as you see that Land of Departure = Castle Oblivion many things should appear much clearer.
The real question is why Vanitas looks exactly like you-know-who while Ventus looks like Roxas.
I'm also confused about the obvious time-loop when Terra is talking to Riku in the Destiny Islands. Why did Terra see that KH2 Riku vision? Why did the young Riku mention something that seems to be taken from KH1 (which supposedly happens 10 years after)?
I hope KH3 doesn't degenerate into a cliche time traveling story.
From what I can guess, KH3 is (hopefully) going to bring the story to full circle. Hopefully the 3DS game turns out to be a non-important spinoff because the story is complex enough and adding more only makes things more confusing.