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Let's see... I like Cyndaquil in PMD1 and since I usually play as female characters, I couldn't be Cyndaquil, so I played as Squirtle and had Cyndaquil as a partner.
In PMD2 Explorer's Of Time, I played as Chikorita and my partner was a Pikachu. I chose Pikachu for a partner for it's Discharge attack.
In PMD2 [3?] Explorers Of The Sky, I'm a Vulpix and my partner is Pikachu. I love fire types and Vulpix is the first pure female-exclusive fire type.
Piplup, Skitty, Shinx, and Pikachu. I haven't been a Shinx or Pikachu, but I still like these Pokemon.
Piplup was pretty good in Explorers of Time, and I think that Skitty was even better in Explorers of Sky.
Eevee has always been my favorite starter, so I was kind of sad that Eevee wasn't available in Time/Darkness. ;-; But I always went with either Pikachu or Mudkip or Totodile! :3