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Question 1: What is a good secondary for MA. I see most people choose SR, would Invuln or WP be good?
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All would be good with MA. All Scarpper combos are good, but MA/DA was voted the least play, but it is still a good combo.
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Question 2: Is MA good for PvE?
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Yes, all Scrapper power are good some better then other but all are still very good.
"All right, they're on our left, they're on our right, they're in front of us, they're behind us...they can't get away this time"- Chesty Puller US Marine Corps
And lest you think otherwise, that wasn't a flippant answer. But there may be a best choice for you, depending on what you want to do with the character. Willpower is a very good choice for first time scrapping, since it's a very friendly secondary with no major weaknesses. Invulnerability is also very good, but has specific strengths (smashing and lethal) and weaknesses (psionic), and will require you to have or gain a reasonable understanding of endurance management. Super Reflexes is probably paired with Martial Arts mostly for thematic reasons, and is late to bloom, but is very solid in the upper levels. Dark Armor seems to very rarely be paired with Martial Arts, and yet would be a good combination because of stun stacking. Basically, you can't go wrong.
I suspect that Martial Arts is generally considered the weakest of the primaries. The secondary effects seem to lack a cohesive theme, and the damage output is just middle of the road. Some people also don't like the all kicks nature of it. But if you don't mind doing nothing but kicks (or adding punches from power pools), the weakest scrapper primary honestly isn't very far behind the strongest scrapper primary. I don't want to scare you away from it. It's totally fine.
"That's because Werner can't do maths." - BunnyAnomaly
"Four hours in, and I was no longer making mistakes, no longer detoggling. I was a machine." - Werner
Videos of Other Stupid Scrapper Tricks
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And lest you think otherwise, that wasn't a flippant answer.
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I had to look that word up 
And Werner is right it wasn't, but I could see how it could come off that way. I don't always write a lot when I post, my answer are short most of the time.
"All right, they're on our left, they're on our right, they're in front of us, they're behind us...they can't get away this time"- Chesty Puller US Marine Corps
For question one, any secondary can work well for Martial Arts. The only real factor in choosing a secondary is knowing how to use it.
For question two, yes, Martial Arts is very good for PvE. To agree with Werner above, Martial Arts may arguably be the weakest of the Scrapper primaries, meaning that there is no one single trait that distinguishes it above other sets, but hell, it's still fun and very viable. I know there are some MA players who can complete the RWZ Challenge, solo Pylons, and solo AVs.
1) All 3 are good, SR is my favorite scrapper secondary partly due to the very quick combat mobility. Swift + Quickness + Sprint = running circles around the enemies. Both SR and WP, and for the most part Invuln(Except Dull Pain) are fire and forget secondaries. Just Toggle them on and go have fun attacking. I personally prefer SR and WP as well as Shield Defence due to the fact that I prefer a secondary set that does not require me to pay attension to timing clicky powers or having to devote attension to active defence outside of using my mobility to best position myself. I prefer to toggle up, wade in , and generaly have fun with the offensive side of the character.
2) All scrapper power sets are good in PvE, its just a matter of personal playstyle. My playstyle lends itself best to SR fire and forget sets like /SR.
I'm sorry if these questions have been asked before, I just wasn't able to find a guide.
Question 1: What is a good secondary for MA. I see most people choose SR, would Invuln or WP be good?
Question 2: Is MA good for PvE?