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If I had to pick one, I'd probably pick Aron. Not only is it adorable (in it's own kind of way, haha), but it eventually evolves into Aggron, which is one of the more badass Pokemon of the generation as well.
Some other favorites of mine from Hoenn (in no particular order) are the Treecko family, Tropius, Shedinja, the Gardevoir family, Sableye, Breloom, and Rayquaza.
In my opinion, Generation III has the BEST Pok?mon. The designs were so fun and decent overall. In fact literally every Pok?mon in this Generation I like.
But my most favorite has to be Skitty. She was my partner in PMD:EoS, and I just love how the Pok?mon itself is a kitty.
Exploud and Milotic here. These two are some of the most memorable Hoenn mons for me. Exploud has STAB Boomburst and is insanely badass, while Milo has good general utility and an amazing design.
My favorite would be Mudkip. It's my favorite water type starter Pokémon and is rather cute looking lol. My other favorites would be Latios, Latias, Beldum and Jirachi.
Where do I begin? There's Aron, who's actually pretty cute but evolves into quite a powerhouse. Treecko, who's design I just love. in general, the Hoenn starters are my favorites with me having played all three starters multiple times (I have played this generation quite extensively; the only other generation that I've played more is the fourth gen and perhaps the sixth with multiple replays of Y, Alpha Sapphire and even Super Mystery Dungeon). Latios and Latias as well are pretty cool, not totally OP legendaries.
Mightyena, who carried my team through a particularly intense Sapphire run, and wormed itself deeper in my heart after OR's Elite 4. Aron, Lairon and Aggron because their designs are top-notch; I have a thing for heavy armor designs/looks XD. Crawdaunt, whom I couldn't really get into at first, grew on me after struggling to find a Pokémon with False Swipe~
Mawile and Zangoose and Masquerain! I love all those. Just still bummed that I can't get Mawile and Zang in AS and that Masque isn't a water type, haha.
Sableye and Blaziken and many more are also pretty cool.
Right now, my feelings for Skitty are starting to lessen, and there are some other Pokémon I'm in to, like Roselia, the Ralts family (even Gallade), Shelgon, and Vigoroth.
I think my name makes it obvious.
my next 4 favorites arer also from hoenn (lol)
Torchic, absol, altaria, delcatty
I also like the lotad line.
Oh yeah, and the ralts line.
and the shroomish line, and sableye, duskull line, lileep line, flygon line, cacnea line, barboach line, milotic, the legendarys and