The species names are all stored in the game text narc; you can use PPRE's text editor (if it doesn't have one, use SDSME instead) to change them. You'll have to scroll through a long list of text files to find them, and there might be multiple copies of the file that need to be edited.
You can add new Pokemon to the DS games, but it'll very difficult unless you really know your ASM.
This post is the only publicly available information on how to do so.