When it comes to PvP, PvE conventional wisdom regarding the individual sets and powers goes right out of the window.
In PvE, Katana is generally the better set. I think they both have comparable DPS and burst (I can't recall numbers, so please correct me if I'm inaccurate), but Katana has better AoE capabilities and Divine Avalanche's defense buff tends to be better damage mitigation than MA's stuns.
But in PvP, it seems that MA has gotten more popular. MA probably has better burst due to EC's animation time, and the stuns tend to be more useful than the defense since there is no mez protection in PvP (just mez resistance).
Most of the information on this board tends to revolve around the PvE game, but that doesn't always apply to PvP, and it's better to check those boards to see what trends and strategies work in general, and then apply that info on a scrapper build.
I was all set on making a Katana/Elec for I16, (for pvp I might add), but after seeing someone post how they beat Katana's with their same secondary Martial Arts, it made me think.
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Are the stuns better than the def boost? (DR makes me think loldef so thats a potential strike agaisnt Kat)
Which side produces better dmg per second and which does better burst dmg?
Which has a more damaging Attack chain? (or Which go go through it faster thus creating more dmg) For Katana it would probably go SotW->DA->SD->DA->GD->DA, for Martial Arts it could either go EC->TK->CK->TK->CaK or SK->EC->CK->CaK. Or course I don't know if LBE from the body mastery is a good power to substitue a reg. attack chain power with, I would doubt it with Katana with all the Redraw it would cause.
And just a fun question, which set (Katana or Martial Arts) looks cooler? I've heard great things from both about this, and I can vouch for Katana up to Soaring Dragon (deleted him at 30, was a kat/regen, don't ask why...
Those are the questions that came to my head right away. And if you don't pvp with them share your pve experiences, they're very similar in the question im asking (except the first, sorta)