MA, as someone who stalked an MA/NIN to 50 and couldn't find enjoyment in any other primaries, it's damage is decent. It's focus is single target, more or less like Stalkers themselves are.
I like it a lot on my stalker, but I didn't enjoy it on a scrapper. The most important factor isn't it's overall comparison numbers wise to other sets, but your personal enjoyment of it. I liked it because I could change the attack animations with each of my costumes to add more depth and variety in battle. You may love that too, or you may want energy melee or dark melee's 2 damage type per hit attacks.
MA does have one advantage over some of the other sets and I had to do research after someone pointed it out to me and I didn't believe them. It has an inherent accuracy bonus like weapon sets, or more accurately, more like Archery's in my experience. I almost never miss when my feet go flying at the other guy's face.
MA does get an accuracy bonus, but not like Archery's, IIRC. While MA gets the accuracy advantage like other weapon sets even though it isn't a weapon set, Archery gets an added bonus ontop of being a weapon set.
As for Stalker MA, I tried it and got to 26 but I couldn't play it. Mainly because there's no Dragon's Tail animation...and I don't mean that it lacks the PBAoE attack...no, I just love that sweep animation so much, I couldn't play the set without it.
The set is pretty solid though. It hits hard and fast and has one of the coolest AS animations.
All sounds good to me, and I'm having a blast on it right now. Only level 12 so far but loads of fun, and very pretty to look at. I'm suffering badly with endurance though. Got end reducers in all attack skills and toggles, and it's still iffy. 
Guess all that will change once I hit 20 though. Temporary issue.
I remade my level 43 MA/SR Scrapper as a Stalker and took her to 50. I loved it. I missed Dragons Tail a bit at first, but the combination of hard ST damage and control was great.
I havent played a Stalker with AoE attacks though. that experience may spoil you for St sets like Martial Arts, I wouldn't know.
I created an MA stalker, just because I wanted MA - it fit the char I wanted to make. I just realised yesterday though, that ALL attacks are single target. There's no kind of aoe, cones or anything of the sorts. Nothing.
Now, I don't mind that personally. I think it's kind of cool but: Does the MA dish out enough single-target dps that it makes it a competitive option compared to the powersets that do have aoe?