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Substitute just seems to waste a turn that could be spent setting up. Opponents almost always break the substitute in one hit.

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I'm not that well-versed in Smogon sets, but I think they use Substitute to block Thunder Wave and Will-o-Wisp. It's probably easiest to set up when they force a switch.
What about Nidoking? It's immune to thunder wave and toxic, and will-o-wisp doesn't cripple it.

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Best answer

I'm going to answer the basic reasons. People might have their own reasons based on how they think or play, but these are the standard ones.

Substitute eases prediction. This means that predicting wrong with substitute doesn't amount to much, and predicting right can put you at an advantage. If you had say, terrakion with substitute against garchomp. Garchomp might expect you to switch or it will set up rocks. if either of those happens you can just set up and attack. However, what if the Garchomp just used Earthquake? Well, you put your sub up, so you don't get KO'd. If you didn't have sub however, you would have just been knocked out. So why not use Protect? Well, if you can get your sub up and have it not blown down again, it puts you at a significant advantage, giving you extra turns to set up, attack right off the bat or avoid status. But if you used protect then there's no benefit if nothing went wrong. Protect only helps you in one scenario, not both like Sub does.

The other is to simply avoid status moves. It'a annoying to get paralysed or will-o-wipsed by a wall you can't break through. So just set up a sub and swords dance 50 times first. They can't do anything except switch out or hope for crits.

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B-but 3 is the maximum amount of times you can swords dance advantageously.
Apparently you've never seen a Doublade river dance o.O
@Aranacana it's called PP stalling. If you don't know about it, you'd better learn fast.
I was actually joking .-. I've never PP stalled any move with more than 8 PP kek
So...you never had an opponent who complained about having to go to the bathroom? Every Pokemon nerd should have that on their bucket list.
@Doctor Disco @sumwun

I was just joking guys, don't worry.
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When I was playing Omega Ruby, I did a battle test (It was against CPUs, but it's related). One of the trainers had a Scraggy with Focus Punch (and substitute, among other things). Usually I just use Fly and say goodbye Scraggy, but here, it used Substitute. It held for that turn and the next one, and on the next turn, it used focus punch. While it tightened its focus, I defeated the substitute. Then, focus punch kicked in, and well put that in a loop, and I lost. Badly. So, anyway, that might be why. To not flinch while using focus punch.

answered by
Focus punch is pretty rare and almost never good in competitive battling. The reason why you lost to it is because you used fly. Don't use 2-turn moves.
Thanks for the tip! Although I don't actually have a Pokémon with fly in Omega Ruby, only in Y, and even then, only one Pokémon knows it. I mostly lost because of the substitute.
If you were relying on a move other than fly, then you wouldn't have lost so quickly. Don't use 2-turn moves.