Overall PvE game is Electric/Nin. Do you plan to use IO's? If not then I'd probably go with SR (with aid self) as you will get higher defense.
The stalker's assassin strike makes the godly aoe set that is electric an all-rounder, as opposed to the other melee versions of it which lack significantly in single target damage. Only power I consider skippable in electric melee is Havoc Punch; you will want to figure out how to put everything else in, srsly. Skippable powers in ninjitsu would be Smoke Flash above all, while caltrops can have its uses, but is skippable for tight builds, and so is Kuji in Retsu (hopefully you are getting yourself softcapped with IO's).
Ninja blade and spines are both good primaries, but they're also mostly lethal damage, which is heavily resisted and you will be able to tell the difference in upper level play. Plus, if you take Ninja Blade, you have to figure out how to leverage some aoe damage out of it, since the set only gets one pure aoe attack. That said, I have one of both in the 40's (Spines/Nin and Nin/Electric [don't recommend that secondary unless you really know what you are doing, and then only with Ninja blade or Broadsword, and significant IO investment]).
DM is nice single target-wise, and negative damage is awesome, but it lacks so miserably in aoe that you will not be as useful on teams.
The Inspiration Maker's Guide [i12] UPDATED with POPMENUS and Movement Binds!
A Flash in the Dark: The Electric/Ninjitsu Stalker [i23]
Kheldian Inspiration Macros UPDATED with POPMENUS and Movement Binds!
Guide to the Katana~Ninja Blade/Electric [i23]
I will use what IOs I can, but do not have that much infamy. I can probably get the knockback protection chip from Karma...
Well, kb protection is the only status hole that ninjitsu has, so that's good. If you can't manage the sets to softcap with nin (these IO's aren't the most expensive by far), you can still go with nin over sr if you use defense insps. Otherwise, I'd rather have higher defense. Other than that, elec, nin blade, and spines all have significant knockdown in their attacks, which helps mitigate damage a lot. Or if you don't want to work with IO's or insps, but still want the high defense, go with ninja blade for Divine Avalanche.
The Inspiration Maker's Guide [i12] UPDATED with POPMENUS and Movement Binds!
A Flash in the Dark: The Electric/Ninjitsu Stalker [i23]
Kheldian Inspiration Macros UPDATED with POPMENUS and Movement Binds!
Guide to the Katana~Ninja Blade/Electric [i23]
I agree with Micro. ELM on a Stalker is 10 times better than a brute/scrapper.
I love my EM/Nin Stalker and I'd roll an ELM/Nin, I have an ELM/Regen just because I'm a bit tired of /Nin.
Since Ninja Run came out, I went stereotypical and built a nin/nin Stalker with the appearance of a modern-day ninja. It's pretty fun, and the stacking def move (forgot the name) helps keep me alive in prolonged combat.
I'll probably try out the elec/whatever Stalker sometime soon if people are saying it's that good though, haha. 
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Quote:
If you just do the content and use those merits you will earn intelligently, you can easily put together a multi-billion inf build by the time you're level 50. As soon as you get some inf, put in some low ball bids on the IO's you want, and you don't want level 50 sets (other than purples) if you plan on malfactoring at all. The biggest problem I had was storing all the level 35 to 40 IO's I bought untill I could slot them.|
Originally Posted by Torrentor
I will use what IOs I can, but do not have that much infamy. I can probably get the knockback protection chip from Karma...
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You can fund yourself with just a little bit of work, with your merits and the drops you get doing the content. Really. Don't be put off by the "buy it now" price tags you're scaring yourself with, you do not need to pay those prices. (Except for the PvP IOs, so don't bother with them. For now
) You can do it, just give it a try, it will be fun!
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Quote:
IOs are cheaper than SOs.|
Originally Posted by Torrentor
I will use what IOs I can, but do not have that much infamy. I can probably get the knockback protection chip from Karma...
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Cost to use SOs from level 22 to level 50 per slot: Average 250k
Cost to craft a memorized level 35 common IO: 60k.
Cost for crappy set that is higher % than an SO: level 26 acc/dam multistrike: 39k to craft, you can buy the recipe sometimes as cheap as 100 (not k, just 100 full stop) inf, salvage Iron, Rune, Symbol should be less than 2k inf to buy. Total cost: 45k or less.
You can afford IOs. Ignore purples and others. Get the cheap ones. That level 26 Acc/Dam multistrike gives 21%/21% bonus. If you have two acc/dams slotted that's 42%/42%. If you have one Acc and one Dam level 53 SO you only have 38%/38%. So a 45k level 26 IO is slightly better than a level 53 SO and way cheaper.
I dunno, 45k compared to 250k, plus higher bonuses and maybe a set power or two, plus you don't need to worry about it expiring...
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I am making a Stalker, and in researching the forums I have narrowed things down. But there seems to be a great debate about which is better, so I am asking advice...
I will only PvE with this toon, as I do not play PvP. I will solo and group about 50 / 50. I would fight AVs if the build can handle it, but probably only with a group...
Most people say Spines is the best. I also hear a good debate for Nin, DM, and EM.
As for the secondary, Nin or SR seem to be split 60 / 40 on people's prefrence.
What's the best overall? Also any suggestions on powers to skip would be helpful. I am more experienced with blue side than red...