You've pretty much summed it up there.
SR also waits until 35 to get any AoE defence out of Hide.
It has better Defence and also close to 90% Defence debuff resistance once you slot everything up.
Super Reflexes
-More defense. With Tough (with a Steadfast +def IO), combat jumping and Weave, and every +def power you have 3-slotted for def, you're softcapped.
-95% Defense Debuff Resistance. You must slot everything that gives DDR to the ED threshold to see 95% on a stalker.
-Quickness
Ninjitsu
-Slightly less defense. More set bonuses are needed to softcap, or doing something silly like taking CJ, Stealth, Weave and Maneuvers.
-Fewer toggles. This saves on endurance, especially if you plan on scrapping.
-Unenhancable Defense Debuff Resistance. Like all defense sets other that SR and Shield, You're stuck with the base value. It's been a while since I played Ninjitsu, so I can't remember how much you get, but it's not as much as SR.
-Toys. It depends on your play style how valuable Caltrops and Smoke Bomb are.
-No knockback prtection! I have no idea why, but be ready to go get yourself a Knockback protection IO.
The godmode is identical, or at least nearly so, between the two, so it's not really a deciding factor.
Personally, I prefer Super Reflexes. Being able to softcap off just one IO frees up my set bonuses for Recovery and Recharge.
@Roderick
I think that SR has more defense. They both have a great tier 9, and mez protection.
SR has: Quickness. Mini-perma hasten + swift.
Nin has: Self heal + fun but sort of useless toys.
I already have an EM/ Nin which is good, but I'm having some doubts..
And I think that SR would be great for EM because Quickness will help with EM's long recharge times.
I can't decide...