So I've been wondering about this: If Roxas became one with Sora at the beginning of KH2, how did he fight Sora in TWTNW? How did he have a physical body if he had already been combined with Sora? Also, if Roxas had already joined with Sora, what was the purpose of that scene near the end of the game where Roxas becomes a part of Sora? Seems a tad...redundant.
I think the fight was inside Sora's mind, kind of like a revival of Roxas and Riku's fight in the same area. As for the two merging in the end again, I think it was to tie the story together just to make sure the meaning was gotten.