@cmh - The game automatically knows what animations and whatnot to use based on weapon data, but what you need to do for it to work and not have missing body parts is to create a brand new battle.lgp.
In terms of limit breaks, we can use tools to just manually alter all of Nanaki's to be Cid's (which will allow it to not simply be mimicked) or just tell Nanaki to use Cid's limits directly.
Doing the create new lgp method, we can make every single person use Cloud's battle skeleton (and limit breaks) without a single ingame issue, I did extensive testing with this along as redirecting what battle data is loaded for each character.
As part of my test, I made Cloud use Barret's battle skeletons (sbaa, scaa, sdaa and seaa) which enabled me to give Cloud 4 different weapons for a limited character project I did before.
(Only playable characters were Cloud and Tifa, you had the occasional guest, such as Nanaki, Barret and Cait Sith.)
Cloud has Swords (Normal skeleton) Spears (Cid) Guns (Vincent) and Katanas. (Sephiroth)
Tifa on the other hand had tonfas (Normal skeleton) Staves (Aeris) and throwing knives. (Yuffie)
I recalibrated the whole game to allow for only 2 playable characters with fixed materia that went up like traditional rpgs, each weapon had different qualities, such as giving a bigger physical or magic boost, being long ranged, having high accuracy, etc.
Flying enemies were fixed to have almost impossible evasion, so you'd need either the gun or throwing knife to hit it. (or magic.)
While Tifa has more physical ones. (Tonfa) and the magical ones. (staves) and the katana was defence ignoring, and was a mandatory weapon to take down tank enemies, or a spell of the opposing element.
That project was actually a fun one to work on.
And it was easy to have nobody else join the team, I simply used meteor to disable party changes (SO MANY OF THEM) and not enable new additions to the roster, while they could still join for certain bosses.
An example is that in the first mission, Cloud was going solo, then when Barret normally joined, it was Tifa instead and they fought a new boss.
Then for the main boss, Barret shows up and explains that you need a gun or other such weapon to take down enemies like that and joined because we likely wouldn't have won otherwise.
Other examples include when we're fighting the experiment in the HQ, Nanaki will join for the battle.
...Enough about that though, the main point is changing battle skeletons and appropriate data is easy to do and takes a few minutes.