The method I described would allow us to turn either Nanaki or Caith Sith into Cloud's skeleton, although we can do the same for anyone else, such as Tifa, Cid, Barret, Sephiroth, etc.
The way it's done means that there is absolutely no overlap, as we physically change the animations to someone else's, for instance, the game's levels would load the animations aeae.a, aeaf.a and aeba.a for the idle, walk and run animations respectively for Nanaki, but as we changed them directly in the char.lgp to be aafe.a, aaff.a and aaga.a respectively, for every single scene in which the human Nanaki needs to stand, walk or run, he will automatically do it using the respective animations that Cloud would normally use.
We could get him set up to use Barret's animations, but be warned, it is a pain to get his legs properly working.
Doing this method, we can physically change any and all field characters to be someone else (in the main party) except for Cloud and Aeris, because they share 80% of their field animations with NPCs.
Cloud having skeleton A has around 70% of NPCs use his normal animations as well as his misc ones, while Aeris is the same, except a vast smaller number uses her animations, but important characters, such as Hojo and Sephiroth share Skeleton B.
From this, we can interchange Barret, Tifa, Nanaki, Yuffie, Cait Sith, Cid and Vincent between one another by simply changing their field animations.
I have a complete list of what every single field animation does and which skeleton it belongs to, so we can likely implement future mods far more easily in future.
The only annoying part is looking at both lists (Cloud and Nanaki) to see which animations match, then we copy and rename said animation to be for Nanaki, before putting it back into the char.lgp.
I did extensive testing with both Nanaki and Cait Sith as human, and there is absolutely no errors doing it this method.
@Kaldarasha, I never really touched Makou Reactor, but can you use it to physically rename the actual animation files and replace them?
I assumed that could only change them within each scene in the flevel.