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Most of my favourite Pokemon reside in Hoenn, my ultimate favourite is Swellow. Then my others are the likes of Lunatone, Solrock, Altaria, Breloom, Delcatty etc.
Swampert. mudkip is the most adorable of the three, and learning mudslap early on makes winning against anything easy (its like sand attack but does a tid bit of dmg too haha). Also when it fully evolves it murders everything. It is super bulky, learns two of the most common high accuracy moves (Earthquake and Surf) and only has 1 weakness, grass, which moves usually run 60 dmg or lower. I just love muddy water too, its like friggen surf but can also lower accuracy. He's just unstoppable
I'd say the starters, except Sceptile which had a pretty bad movepool, other than that I love Metagross, Salamence, Breloom & Rayquaza just to name a few, I caught none of those {XD} but I saw them kick *** when they're with NPCs, might try to give them a shot in my next playthrough though ;)
Probably metagross. I grew up with gen 3 so there are a lot of pokemon I like from this gen, but Metagross is one of the single most badass pokemon out there.
Altaria. Followed by Milotic, Flygon, Absol, and Delcatty. There are plenty of other Hoenn Pokemon that I also like, but these five would have to be my top favorites from this region.