Twilight can always use more books! She'll appreciate any that he chooses to give her, from ones on obscure subjects (he's in Saffron, so an in-depth look at Psychic-types or one on the history of the Silph Co. would probably be findable) to general texts. If you'd rather not get her a book, she also has a secret weakness for plushies of the stranger Pokemon types. A Magnezone plush in particular would make her day, though she'd never ask for it.

Also, if you have any ideas for things for her to get him, I am all ears! I'm horrible at this sort of thing.