In Pixelmon we try and keep as close as we can to the official size of models. To check what that size is we recommend you visit Bulbapedia. They list all the stats for all the Pokémon that exist. It is possible to use a larger model when creating a model and then scale it down inside Techne using the GIScale property.
Unless there is specific advice to change the size of a model we request that all submissions are in the Pokémon's original size.
It's a good idea to have animation in mind when designing a model as it's hard to implement after creation. You will also find that the way the model needs to be animated will inform the design process (i.e. how many segments you want in a tail, if you want 2 blocks for the main body so that the body can flex, etc).
While Techne supports having lots of shapes all with the same name and renders them happily, Minecraft does not!
Please make sure that all pieces are appropriately named and that there are no duplicate names in the model as this will make the model far easier to implement into Pixelmon.