I think we should do some math. Why are weapon mastery less important for a nuker? Because they are physical based and you're an int heavy character. Regardless of how much % bonus you get by lvl-ing the weapon mastery, you still get more 'overall' bonus by keeping the force (e.g. fire) mastery high, even if you have to sacrifice some weapon mastery. Here's the calculations based on what the 'bonus' meant from this topic (please correct if I'm wrong

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How much bonus in total you get should also be affected by your phy/mag balance. (agreed

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Assuming a typical pure int character with approx. a 1:2 balance:
Phy balance: 50%
Mag balance: 100%
From the character builder, it's actually 52/96 naked at lvl 90; I round off to make math easier
http://bobtheveg.dyndns.org/SRO/Char_Build_Applet/?profile=22653
Build 1 - Fire: 90, Weapon: 65
Build 2 - Fire: 80, Weapon: 70
So how much bonus in total really???
Build 1 - (Fire: 90% of 100% = 90) + (Weapon: 65% of 50% = 32.5) -->
122.5
Build 2 - (Fire: 80% of 100% = 80) + (Weapon: 70% of 50% = 35.0) -->115.0
I'm assuming you get both bonus everytime you imbue (mag) with weapon (phy) skills. If that's the case the overall bonus for Build 1 is higher than Build 2 even though the weapon skill is at a lower mastery.
Does this make sense? To me it's sounds like a case of % of a %; and % vs. absolute values. I think you also feel this too when you play as a nuker that lvl-ing up your weapon skills really doesn't make a whole lot of difference in terms of damage.