Both sets will offer good survivability, but there is one main reason why I would choose ninjutsu for a PvP-build any day:
Ninjutsu offers defense. Defense means being hit less often. Being hit less often means being hidden more often. Being hidden more often means being able to crit more often even if you are spotted (and you will be spotted in higher zones). And being able to crit more often means winning more often. 
If it has eyes, you can blind it, if it has blood, you can make it bleed, if it has a mouth, you can make it scream.
i sense a pattern 
but tbh your right but that is assuming your foe doesnt have high acc but at the same time im not sure how common that is in PVP
also i just thought, with hide and /nins 2 main defence toggles how many luck ins would i need to counter someone with tactics or focused acc?
ninj is a fun set, you have no kb protection so will have to get acrobatics for pvp imo.
You can bypass defence, you cannot bypass heals
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EM/Regen is a bit flavour of the month ATM.. see loads of them around, mainly due to massive damage potential and PvP survivability.
For PvE I find defence based secondary much more satisfying.
stalk, u just mentioned my main concern
how easy is it to bypass /nin defences
wat powers can bypass its defences
and most important, if you have a defensive set, how offten are your defences made useless in PVP?
if its as often as i fear, i might as well re-roll an EM/regen 
Fear Blappers mainly, Aim+BU=162.5% accuracy increase, cue a really painful series of hits in a small space of time and likely one dead stalker at the end if you dont pay attention and react duely.
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stalk, u just mentioned my main concern
how easy is it to bypass /nin defences
wat powers can bypass its defences
and most important, if you have a defensive set, how offten are your defences made useless in PVP?
if its as often as i fear, i might as well re-roll an EM/regen
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sadly its pretty easy to bypass ninj and even sr, blasters with aim and BU can do it at will and most of the time 2 acc SOs + BU means scrappers will too, factor in focused accuracy and it gets even harder. I dont take defences on my stalkers and play as if people can see me, keeps you sharp 
.
Given the low hit points of a stalker (less than a blasters for a melee toon) dull pain is a godsend.
EM/Regen is my advice
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Its your fault
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ninj is a fun set, you have no kb protection so will have to get acrobatics for pvp imo.
You can bypass defence, you cannot bypass heals
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Ninjitsu gets a selfheal which imo is identical to reconstruction. They don't get dull pain, though.
ps. So far I have met very very few defenses that I can't bypass with my blapper (Im not entirely sure have I met any at all but I can't remember so I state my words carefully..) so I wouldn't worry about that one.
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i no that at high lvls /nin defence can be over come by per+
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No stalker hide gets beaten by someone with high perception.
Defence gets beaten by every man and his dog having tactics+FA in the high lvl game ie accuracy
Defiant's GoEH/MILITIS METUS
*starts rolling an EM/regen*
thanx for the advice guys, helped my deciding a whole lot quicker
i was thinking of making a EM/nin toon for PVP but im not sure if regen would be a better choice.
i no that at high lvls /nin defence can be over come by per+
however regen means i will get hit alot...
can anyone with experience tell me how these two sets fair in sirens call, warburg and RV
and i no every body says "no set is the best" but in PVP situations, which secondary will increse my surviabilty