Inter-Pokemon crossover ships!
Yes I know you're confused. Pokemon is a nebulous franchise and as such covers a wide variety of continuities. The games, the remakes of the games, the show, the billions of manga series...heck, even the card game has some semblance of a canon.
So who do you ship between the series? If a character has multiple incarnations, state which one you mean (unless you mean more generally).
I want to see Hareta (DPA! manga) and Sapphire (Special manga). I think it would be adorable and involve much swinging on vines.
Also K-2 (DPA!) and animeverse Gardenia. They would have so much to talk about! Most of it inappropiate for children!
And I'm not sure if I'd ship it, but seeing Wally (games) and Peanut (Magical Pokemon Journey) meet would be one of the cutest things ever. They'd be sick buddies!