Emi
Each approach has its ups and downs, so if you choose to separate the skeletons, you will have to reimport the same animations across all skeletons and apply the tweaks. This can be an advantage if you plan to have not many animations but lots of customization in your files. Vice-versa, if you won't have too many characters, but lots of animation, the effort in using a single skeleton is worth it.
Considering what you're doing is pixel art, that usually has fixed angles in its pure form (0, 90, 180, 270 of rotation, translating items only at full pixels or half) there can definitely be advantages in importing animations expecting less tweaks.
If you're using a hybrid approach (the base art is pixel art, but you don't care about keeping pixels at an angle, or will later apply a pixel art filter) then it means that you will be able to animate freely, but given the odd angles you may get, the matching may not be as precise and therefore reliable.
Emi My understanding is that if I animate the bones, the animations would look the same for characters that are physically different. I could just change the length of each bones to match new characters’ body parts.
While it's true that if you reimport an animation, it will add the same amount of translation/rotation/etc. to a child bone, but keep in mind this is relative to its setup pose.
Ultimately, the length of a bone does not matter for animating purposes, only for IK and path constraints as it's used by these to calculate the bones' postions.
So you could also not change the length of a bone, it's more important to change its position technically and broadly speeking.
Emi While if my animations are solely based on keying in IK’s positions, I will then need to re-adjust each animation’s IK’s positions for different characters.
It depends, sometimes all that's needed is to reposition an IK target in setup and that's it. Sometimes the target needs more tweaks.
I think the amount of work for IKs would likely be similar both in a single skeleton or multiple skeletons situation.
As for bones themselves, you'll need to tweak their animations in both cases as well, the real question is:
is it going to be more time consuming to add new skins or to add new animations in the long run? and that should tell you which approach to pick.
If you have to constantly add new animations, don't separate the skeletons, if instead you have to add tons of little hats, different body shapes etc. do separate them if you like your sanity.
