I might have already posted here but if I have I completely forgot, so I'll just do it.
In my first Red Rescue Team game I had Mudkip and Torchic. In some later saves I had different ones, including one time I said I was female in the questionnaire so I could get an Eevee.
In Darkness I got Squirtle and Charmander. Or that might have been another save file and I might have had some different ones the first time. Then in Sky I started with Riolu (for obvious reasons) and got a Mudkip as my partner.
By the way, since I saw some earlier posters in the thread say PMD3 to refer to Sky, that is incorrect. PMD2 includes Time, Darkness, and Sky, just like how Generation 2 includes Gold, Silver, and Crystal.