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Well, I sent my metagross over to poke pelago, and gave it 40 sp. def sessions. This should even up the defence and special defence right? (Cuz def=130 and sp. def=90 of metagross) But it's defence still exceeds it's sp. defence. It has more IVs in sp. def. What's the issue?

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Poke Pelago sessions raise the Pokémon's EVs, not their base stats, which, as you stated, is 130 and 90, respectively. Base stats influence the final stat for a Pokémon more so than EVs and IVs, so, even though your Metagross may have more EVs and IVs in its SpD than in its Def, it's base Def stat is just that much higher that it's still more bulky on the physical side than the special side.

For a more in-depth explanation, non-HP stats are calculated using the following formula:
image
What this means is that, (disregarding the nature), every point of the Pokémon's base stat will give 2 points to the final stat, while every 4 EVs give one point (when at Lv100). So, theoretically, you'd need at least 320 Evs in SpD to match the Def stat, assuming IVs and Nature are the same for them, which, as you probably know, is impossible, since it exceeds the 255 EV cap. Metagross' SpD stat can only exceed its Def stat if it has higher SpD EVs, and either higher IVs, a +SpD and/or -Def nature.

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But since it gets 160 evs in sp.def through poke pelago, proportionately it must get the same stats in both, right?
Stat changes update with level-up, and your IV's can be different. You may also have taken it to battle and it gained def EV's. Or it could have max EV's and be incapable of gaining anymore :P
Ah, I think I see the confusion now. I updated the answer with the actual formula and an explanation that (hopefully) clears this up.

Also, @Stakatacool, since Gen 5, the Pokémon's stats update whenever the Pokémon receives EVs, rather than only when the Pokémon levels up.
The last para clears it up, thanks!
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