For Kuja at his end in FFIX he ends up saving everyone and becoming a good guy kinda, so that would be the reason he is on Cosmos.
Cloud- I think he is just being used like normal by Sephiroth.
Terra- Easy. Mind controlled by the clown.
Tidus- as stated it might be Shinyu and to ask why Shinyu looks like Tidus is cuz Tidus is just a dream right? Well they stated he is a Dream of Shinyu, thats all they went into it. So its either Shinyu or its just because Jecht is on Chaos and seeing as this is infact a prequel to Dissidia 1 the daddy issues are more then likely still around.
Jecht- He was a good guy so that one is easy too.

I would like to see more change ups too. Like Cecil has said to be a Chaos warrior in a cycle, it would be interesting to see Sephiroth Cosmos for a cycle but that would be more of Crisis Core Sephiroth so maybe we should replace Cloud with Zack for that one.

As for FFXI How they are adding Prishe as another cosmos warrior I would of liked to see The Shadow Lord or something for a Chaos warrior from FFXI.