It never gets old when people keep saying this, knowing that it's wrong. Player set-up is only ONE element, but that's completely random as you have no idea what the player will use. Especially with such a large and expansive dex at your fingertips. It does not determine the difficulty at all and doesn't change the base design of the game. This is like saying choice of weapons in Zelda determines how easy or difficult a game is, when in reality, boss patterns, movement, damage output may still be difficult even with the weapon choice in mind. Or more closely, it's like people who say turning off the Exp Share or using Set mode makes the game harder. They don't because they don't take into account that the AI is still shambolic even with Exp Share off/Set Mode on.
Keep in mind that Game Freak has a bad habit of gimping their AI for no reason. XY has their gym leaders use a small number of Pokemon + choice of Pokemon (gym leaders in previous games has used quite powerful Pokemon) + 3 moves up until Gym 7 (and even then, Wulfuric has one Pokemon that uses only 3 moves).
TLDR; People need to stop acting like limiting yourself is what determines the difficulty of a Pokemon game. It comes down to the base design of the game, as well as, how the gym leaders are designed.