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Squirtle joined the Squirtle squad to help out his friends. It's not too much of a different situation.
Yes, Squirtle joined the Squirtle Squad to help out its friends, but there's a key difference between that situation and Goodra's. Squirtle wasn't stuck in just one place. Being the leader of the Squirtle Squad would require it to go beyond just one area to fight fires and train the other Squirtle. We have seen that Officer Jenny is able to bring it to Ash at least to Johto and Kanto when he was in the Battle Frontier. Goodra's situation isn't that similar. It is in the wetlands and there is no indication that the keeper of the wetlands has its Pokeball or that Ash could contact him to get Goodra back like with Officer Jenny.
Sure, both Pokemon left to help their friends, but that's really ignoring the key differences in their situations to make Goodra's situation sound more different than it actually is. Squirtle did leave to help its friends, but through training as their leader rather than staying behind in its homeland to protect its friends. If they just threw that scene there as a cameo to remind the audience of Goodra instead of bringing it back, I'd be fine with that.