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>Team balance
I usually stuck with balanced teams of six, but now I'm making teams of five. The next point elaborates on this.
>Using HMs
Both points, pic related. Only one HM Master. I'll distribute the rest of the HMs among my team, making sure they fit well in their movepools. The game is a lot more enjoyable if you don't have to go back and swap your team around at the PC every time you need to to use anything that isn't named Surf or Fly.
In Gen 7's case, I'm free to make a team of six.
>Catching Pokemon
I just keep the Pokemon I wish to use in mind. Less experience points are wasted this way. If I'm forced to use a Pokemon to get by (e.g. a Nidoran to get by Brock and until I can catch a Bellsprout in Pokemon Yellow), then I'll box them after they serve their purpose.
>Pokemon availability
I only use Pokemon found on the cart. No trading.
>Shift or Set
Set, of course.