Hearts vs. Souls and why nobody understands the plot of XIII-2 and LR

By all means, this is not the problem but not differentiating between what is paradox and not. Heart and soul is an overall foggy concept anyway as already shown in Kingdom Hearts often enough. Such psychological or spiritual terms very often can be used similiarly or with slight differences. Just as your essence, your individual existence basically is your consciousness, which can also be called the self or depending on how we define it, also can be called the soul. And - in Kingdom Hearts is even directly connected to the heart - as Heartless are the original individual of the somebody since the consciousness lives on with the heart (or is actually the heart as well as the heart is emotions and such).
In the end it is not hard enough for major misunderstandings. Also the plot of Final Fantasy XIII was still understandable - even if we just consider a Western version. Really only paradox things are what causes problems.

Things like "Yeul is the core of a paradox because many love Caius and one loves Noel" are what is problematic as that itself is not actually a paradox (because even if they are the same soul they still are their own individuals meaning it should not matter just as you and your past self are while connected own individuals nonetheless - but maybe sharing one soul was already enough, such things are what is not explained enough). All in all such slight differences are not the problem. You normally should still understand it - of course most still don't. However, yes, very unclearly explained, similiarly used words can cause misunderstandings, that is however, because it is very normal to not totally use them without connecting them and their meanings. They are very similiar and depending on the situations often used equally. You can try to explain the reader what is meant but often you yourself don't even make an actual difference.

Oh and what people did not understand about Lightning returns was the ending and that everything would have been destroyed through Bhunivelze. He wanted marionettes and so destroy the individual existence. Also that Lightning and the others wereb reborn but with their very own consciousness and memories. It was them, their consciousness nonetheless, not a new being (like clones would have their own consciousness and a copy of memories but here it was not a new individual consciousness but simply their own as it was their very own, original soul). So nothing to hate about but actually the best ending Final Fantasy has ever seen.

So basically, the story is understandable and great.