They're not 100% different skeletons. Every single character is built with the same joint hierarchy, regardless of shape or size. The only differences in skeletons is joint placement in 3D space, and additional joints added to the end of the hierarchy if needed. You can, right now, go into Smash 4 and mod spinning kong on to Duck Hunt and he'll do the animation. It'll look stupid, but it will function. And that's without joint retargeting.
Joint retargeting is the technique that every modern game uses to allow the same animations to function on characters of different sizes. This technique does not shift the retargeted joints in 3D space (like you get when porting animations in Brawl, which gives you Ganonchu), it only reorients them. This is why in an online game with customizable characters, they can all do the same canned animations, or how Andy Serkis, a human shaped human, can perform motion capture for a chimpanzee.
Basically, it's like this. You take an arm. At it's most basic, it has three joints. The shoulder, the elbow, the wrist. You have an animation of a character with a long arm, and you want to port it on to a character with a smaller arm. As long as they have the same joint hierarchy, which all Smash characters do, you can retarget this animation on to the smaller model quite easily, and there's even math involved that can compensate for the fact that the joints would need to rotate less on the smaller arm to reach the same position as the longer one.
It's actually not nearly as much work as completely reanimating everything Dark Samus does. This technique was invented in the first place to save time.