Well in most pokemon fics, sequels would be pretty boring if you don't spice it up. Don't just have the hero go on another big adventure in some other region. If you're not a writer of excellent calibur then it would be hard to write a series in which the good guy wins in some adventure in every book. Most succesful series either have the good guy lose in some books, or have just one continuing story, without the antagonist being defeated, like in the "Inheritance" books.
And another idea for a series...Have the same setting, and have the story continue, but with time gaps. The characters will be older, and play different roles. Perhaps even a new character will have the role of Protagonist. The best example for this one would be a movie, not a book...StarWars. From trilogy to trilogy, the Protagonist, Anakin, becomes the Antagonist, Darth Vader, while his son Luke becomes the protagonist.