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I'd love Inkay and Gourgeist to stay, and I don't think it is unlikely, as they only have one Pokémon each (excluding Wobbuffet, which I believe will stay), so they can have Inkay and Gourgeist and still capture new Pokémon. They left they BW Pokémon with Giovanni and they left their DP Pokémon at the headquarters because, I believe, with that number of Pokémon it would be hard for them to capture new Pokémon. And that is not the case now, so I really hope they get to keep them. Moreover, Inkay and Gourgeist are way more developed than Yamask, Woobat, Frillish and Amoonguss ever were (well, except maybe Yamask, but he was only developed during its first episodes).
However, the fact that they once told Giovanni that they have captured Inkay and Pumpkaboo for him makes me think that, unfortunately, they will leave them with him (even though what they said wasn't entirely clear and objective).
And I still have hope that, somehow, someway, Seviper, Carnivine, Yanmega and Mime Jr. get to return, even if just for Team Rocket's final battle against Team Flare...
