Recommending +40 haste/crit over +40 agility gem

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This doesn’t seem right. Shouldn’t the +40 agility gem always get better parses than the same amount of a secondary stat?

They are so close in value that you could go with whichever gem you prefer. If you look at the gem list, you will see that the optimizer estimates them within 0.01% of each other: for all practical purposes, equal.

If I run a quick simulation as another set of data points to back up the optimizer:

Your gear with agility gem: 16,246 DPS
Your gear with crit gem: 16,266 DPS

The crit gem simulated slightly higher, but the difference (20 DPS) was below the margin of error of this simulation (about +/- 40 DPS). So “too close to call”. Use whichever gem you prefer.

If you set the gem+enchant threshold setting on Best in Bags to 0.25% or the default 0.5%, it won’t tell you to change your gem – this setting is there precisely for cases like this, where changing the gems is such a tiny theoretical gain that it isn’t really worth the gold to do so.