PokéBase - Pokémon Q&A
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Take a pokemon with a quiet nature meaning better sp.attack and worse speed but for its IV its likes to run.

Will its speed be higher or will it still be below or will it be neutralized?

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It depends on the Pokemon and their maximum/minimum stats.

IVs are a hidden value out of 31, so at level 100 a max IV Pokemon would have 31 points more than a 0 EV Pokemon. Natures on the other hand increase or decrease a stat by 10%.

So if the stat at level 100 would normally be 250, then the nature would add or remove 25 points. In that case, good IVs make a bigger difference. But if the stat was around 400 normally, then 10% is 40 points plus or minus, so the nature makes a bigger difference.

In short, IVs matter more if the final stat is under ~300, and nature matters more if the final stat is over ~300.

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I have a Mega Rayquaza and it has a maxed IV (31) on atk, sp. atk, and spd, but the nature is calm and I have another with naughty nature and it has 2 IV on atk and 16 IV on sp but its EV trained and got 171 EV on atk (360) and 90 spd (219). Which is better?