I think it was since the kids were both royalty and potentially Force sensitive, they were separated to keep them away from agents of the Empire who’d use them as political pawns, and away from Vader, who would train them as Sith. Splitting them up so an heir is more likely to survive might have been the thinking. Also, if they raised twins, Vader might someday muse on, gee, that royal family is raising twins who would be the exact same age as the kids I would have had if Padme lived…
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