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I don't really like to nickname my Pokémon in my games. There are exceptions to this of course. I like to nickname the Seedot in my Emerald and I nickname all the Pokémon I use in challenges.
I almost never nickname my Pokemon. I sometimes rename my HM Slaves so that their names suit their jobs. For instance, I had a Lugia that I turned into an HM Slave (it seemed too defensively powerful and too cheap for my main team, besides Aeroblast has such low PP). It's main job, other than to Fly me to places, was to use Surf. So I named it Poseidon. Similarly, my Ursaring whom I used for Dig, Strength, Rock Smash etc was named Ironfist.
I love nick names! Im currently playing through sapphire and my team is....
Scept the Treeko
Mighty the Poochyena
Swell the Taillow
Tad the Lombre
Ectric the Electrike
and Larry the (female FACEPALM) aron
I've never nicknames my Pokes, just a personal preference. I do feel like it could be a clever strategy if you do competitive battling...as in you can nickname your team so the person you're battling against won't know what to expect from you. ;o
I used to give nicknames to my more liked team members but that died down when B/W came around, probably because names stopped being all uppercase and therefore no longer bothered me. XD;