Sometimes I pick a theme, sometimes I don't. At this stage I have so many save files that I literally can't say whether I give nicknames more often than I don't, or vice-versa.
When I DO nickname, I guess it depends on what I nickname my starter. For example in White, I called my Tepig "Piggee" and from there on, everything had "ee" at the end (Like, Haxorus was Rusee, Zekrom was Zekree, stuff like that). Basically I followed the nicknaming format set by the Pokémon Adventures manga, where you pick a syllable and incorporate it with the Pokémon's existing name.
On the other hand, sometimes the initial nickname is a bit too obscure to make a theme around it. In OR, my Swampert was called "Ribo" (based on my original Ruby Swampert - I guess it's just a similar sound to the word 'Ruby' or something, I don't know). But from there on it was free reign for other nicknames. Electrode was 'Blitzball', Swellow was 'Flap-Happy', Ninetales was 'Vixen', Sharpedo was 'Chompy' and my female Breloom was 'Sisbreh'.
And after all that, sometimes I don't nickname at all. I mostly prefer to either commit to it entirely, or not do it at all. Which is annoying because it's all too easy to forget, and end up with mostly-nicknamed Pokémon, haha.
