I definitely name them, probably because I think of them as my friends and partly because I just like to. For example, my current team in Reborn is Lollipop the Swirlix, Blaze the Quilava, Punches the Mankey, Sparkle the Shiny!Swadloon, Lily the Lombre, and Echo the Noibat. In fact, I name every Pokemon that I catch (except legendaries, because I feel like they shouldn't have nicknames), even the ones I don't use.