In earlier generations, my teams were usually the standard 4 + Surfer, Flyer, and an HM slave in the PC. However, now I usually have my Flyer sitting in the PC and, if I have a physical water attacker (Azumarill, etc.), I'll have the Surfer in there as well.
Generally I build my team on type coverage, both offensively and defensively. For playthroughs, I consider my team a success if it has great offensive type coverage whilst not being frail by any means. I can't ever recall building a themed team, like a Water team, Fire team, etc.