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I want to believe that it's not the end, because in any other situation it'd be REALLY fucking obvious that it isn''t. Characters that have been together for over 25 years now, leaving each other this anti-clamatically? On top of leaving their cherished pokemon just out in a field somewhere? With literally no loose ends tied up at all? Come on, they might as well be screaming in your face that they'll be back to do something else before this ends as a big 'surprise' or whatever.
But that said, Team Rocket have been fucking awful the last 3 years and they clearly have not given a shit about them. That's on top of the anime being particularly bad with ending shit already, so even if they do come back, they could still fuck it up and give them an unsatisfying ending. Somehow, with all the time in the world to get this right, they ultimately won't.
Unless they announce a surprise Team Rocket special or something once episode 11 airs, but i doubt it.