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"Linear" doesn't mean what you think it does. Linear doesn't mean "Not looping back around and backtracking," linear means "There are few, or only one available path to take."
Meaning, Hoenn is as linear as Kalos. You don't loop back around as much (which is debatable, considering the game makes you branch off in a lot of those places), but there is only one path to take, and one order to do everything in. Gen I and (I think) Gen II let you pick the order you went in for some parts, making them less linear. That being said, most RPGs, and all of the Pokemon games, have been very linear. If you really hate linearity, play a Metroidvania.