Having an existing character with similar body structure and proportions goes a long way in easing the animation workload. In Roy's case, his bone structure is very similar to Marth's, reducing the workload on the more mundane and obscure animations (item interactions, ladder climbing, water interactions, sleep, etc) thus allowing our animators to focus more on the main animations you'd see regularly. The similarity in body structure allows us to take one character's movement file (fitxxxxmotionetc.pac) and use it as a solid base for the clone character's animations.
The same principle goes for the moveset (PSA) file; we use a file that best serves as a base for the clone character as build from there. Special Move layout/properties and Articles are the two main considerations here:
- Most specials have properties called Floats that define how that particular special behaves. Changing the values of these floats enables us to change these specials in very big ways; this along with normal PSA coding allows us a great deal of creative freedom in turning it into a different special all-around.
- Articles I suppose can best be described as outside props that characters use within their moveset. Ness's PK Thunder, Snake's Nikita, Mario's Fireball, and Fox's Blaster are all articles; they spawn them when the coding calls for it and then they're removed. They all have their own separate attributes and are notoriously difficult to modify so in many cases we must strongly consider the original character's article properties if we wish to make the clone character use these articles in their movesets. We also cannot add or create custom articles, so whatever the article amount a certain character possesses is the amount we have to work with.
Keep in mind we can use one character's animation file while using a different character's moveset files. So with your Bowser Jr. examples, Nausicaa:
1) Though they're both turtle-y Squirtle's body proportions are pretty different from Bowser Jr.'s and so each animation, even the mundane ones you hardly see, would have to be substantially modified to not look choppy and plain weird.
2) Using Bowser's animations as a base would likely be more suiting; with a very similar body shape I imagine the bulk of Bowser's animations to match just fine after fine-tuning translations to account for Jr.'s smaller size.
3) Bowser Jr. having Mario's moveset files could very well work; that'd mean he'd have access to FLUDD, fireball, cape, and Final Smash articles as well as inherit the coding behind Mario's specials and normals.
So theoretically you could start out Bowser Jr. with Mario's moveset and Bowser's animations and build from there. Keep in mind however that even with a solid base like this the workload that goes into animations and coding is
immense (we're not joking when we say hundreds of hours!); this simply means the huge workload becomes only marginally less... huge.
This of course only scratches the surface on the exact requirements that factor into a character's selection but I hope it helps clear the air somewhat.