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Well I always keep whichever starter I choose in my party.
And I always seem to find myself using an Alakazam and/or a Jolteon. I'm playing through emerald right now and caught an Abra with every intention of using it. Then I decided I wanted to try a new psychic type so I stuck with my Ralts (which is now a Gardevoir).
And with no Eevee in this game, I'm at a loss. I always have one of those two on my team and now I have neither. It's weird.
It's different in every game, usually the first pokemon I catch. (pidgey in kanto, poochyena in hoenn, and shinx in sinnoh.) Obviously Quilava in Johto.
There is one pokemon I ALWAYS try to have in my party, even if I have to go way out of my way to get one, and that's Pikachu.
My Ruby Starter. Swampy the Swampert goes EVERYWHERE with me. No matter what I'm doing, he's ALWAYS in my team. I've really grown attached to him. Playing Pokemon doesn't feel the same without him, so as soon as I beat the E4 I transfer him to the new game. :D He's my favorite pokemon.
If I could have a pokemon out of its ball around me at all times like Ash and Pikachu, it would be a Milotic. I can relate to it. It started out ugly, where nobody wanted it, and then it evolves to something pretty and awesome.
Espeon, of course!
When Platinum comes out, I'm trading mine from Diamond ASAP. That way, he can truly be my partner. Of course, I'll also trade over the rest of my Eeveelutions ^^
My plusle scarlet. On emrald I was going to mover onto diamond but I was too lazy so I was going to do it another time but I'm happy i didn't because now I lost my diamond!
Hmmmm.... I'd have to say Star (why does everyone name Staraptor Star XD) my Staraptor, my Blaziken Blaze or my Empoleon which I cant remember its name XD I usually have a party of six so I guess I have muliple Partner Pokemon. XD
Probably my female Swampert, who was my first Pokemon I ever had the patience with to reach level 100; I tend to change my favourite party Pokemon every play through I do (right now on my Leaf Green, for example, it's my female Clefable nicknamed Puck).