They have different modifiers, yes, slightly, but the base damage is more dominant. Two-handed as opposed to one handeds didn't give as big a boost as their base damage would indicate, but sure as hell they yielded more on the skill side (speaking of mages and pallies here), whether they were worth it is another matter, mostly dependent on the need of extra armor. Things are different in SL where the armor is less crucial. In ao3 I mostly used the glowstick+doll and in bs I started with the wand+bracer but as I got better and the mega staff set got its bonus the staff ruled hands down.
And I've done that research, collected a hefty amount of data for mages (and some for engineers, too). And like I said, weapon speed (or type in general) is a factor, undisclosed and not fully determined afaik, but less dominant than the base damage.
Your anecdote about birds. Well, in balefort birds needed armor. How many death talons (as opposed to shotguns) did you see in ao3? They did lose skill damage, plenty of it. They didn't lose directly the amount of base damage delta, but to say "So most weapons of the same quality and level have almost (if not) identical skill damage" is nonsense, in both games. (cant' speak for nuri's weaponry though)
In PL, and I'm talking about mages especially because that's closest to engineers and most influenced by spell damage, it was always about damage vs armor dilemma. The staff or wand question was answered with what you can survive with, but as for which deals most damage, well it was never even a close call. For a pure int 56 mega gear wand/staff difference was about 10% in spell damage.
I have compared. In SL, especially now with the new gear, the difference is smaller, but still large.In SL, of course the plat rifles do more skill damage. They are premium weapons, and do higher damage most of the time than dropped rifles. Compare skill damage with dropped weapons of various types and same level, and you will find that skill damage is very close if not the same.
And it most certainly is not. It correlates on the base damage.
50 heals with 30 pure int wearing custom atomites, eagle eye and Atomic Dispenser: Average tick was 84.4.
50 heals with 30 pure int wearing custom atomites, eagle eye and Incinerator (+ 28 lim shield): Average tick was 80.5.
50 heals with 30 pure int wearing custom atomites, eagle eye and Bionic Crushers: Average tick was 80.17.
(for the record, the tick ranges are in accordance with those results)
Ok, I was expecting more. The differences were more bigger when I compared the sunwalker gear. But it's still 4-5 %. Well is that a lot? I dunno, but since it's about the same effect as eagle eye, I'd say calling it "close if not the same" ludicrous.
But here's the interesting bit:
50 heals with 30 pure int wearing custom atomites, eagle eye and Black Widow (+ 28 lim shield): Average tick was 83.26.
Now, that is more than I expected. I always thought the black widow seemed to have reasonable stats, and I used it in my director outfit. But the Widow accompanied with the int boost from the shield gave a somewhat surprising result.
I'll post more on this topic soon, because I also did damage infliction tests and damage intake tests. And as I went out to prove that the rifles rule, it turned out they no longer do and I ran yesterday with the Widow and 28lim shield exclusively.
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