This could all be solved by simply putting some dialogue where the professors explain how they produce those candies “with” (and not “from”) pokémon, and that after that the creatures are set free. But noo, let’s just keep it creepy.

From what you said, you shouldn’t be a fan of the original trilogy then. “Completely breaks you from the story and reminds you that it is a film”. The especial effects are not the responsible for it; the plot is! That’s why I saw episode IV for the first time around the year 2000 and didn’t mind about Luke’s…

Dear Mr Rob Bricken, you’re crazy and should read the comics again.