it used to be regen but now i see only that. so.. hum the one i see the least is Energy Aura
I see far more /SR or /EA stalkers in pvp anyway, probably the rarest i've seen on union has got to regen,ninjitsu seems fairly common in pve as well.
Hmm... well I have a regen, but TBH I don't really like him. On paper, regen seems to be miles ahead of anything else (much like one scrappers) but I'm not sure now. SR Has amazing defence, and the +perc is good. Ninjitsu has good defence too, and also +perc, and many useful effects. EA is amazing for solo PvE, as you should never realy run out of endurance, what with conserve power and energy drain.
I think I see ninjitsu the most, and EA the least. I'm trying to make a new stalker, but can't really decide between SR and Ninjitsu myself...
I went SR in the end, I just couldn't fit accrobatics into my build for ninja and I have an EA brute so I didn't want to play that again and regen just wasn't an option for me 
id only take SR because of quickness , other than that compared to ninjitsu it doesnt really do much better :P.
For me to make a stalker, im gonna go with MA but what secondry?
what is the least used set?