It depends on what you want. SR had the ddr and scaling resists to make it more hands off, whereas ninjitsu had the heal and the gadgets to make up for lack of resistance and lower ddr. Both were viable.
Just a note on Stalker SR: Stalker SR was significantly different from Scrapper SR in a number of ways, particularly related to DDR and scaling resistances. Because the scaling resistances were in the passives, Scrapper SR has three and Stalker SR has two. Thus, the scaling resistances were materially weaker in the Stalker set than the Scrapper set, and it would be misleading to think they were 1/3rd weaker: for a variety of complex reasons the actual relative strength was something like half the strength, and on top of that they were being applied to something that had a lot less base health. Normal resistances can be compared at least proportionately between things with different levels of health (I wouldn't, for example, say that electric's resistances were "weaker" on stalkers than scrappers) but the scaling ones don't work that way. Second and similarly, SR's DDR are in the defensive powers and stalkers have one less (6 for scrappers, 5 for stalkers). That means the 13.84% DDR stacks to a base 83% for scrappers and 69% for stalkers. With slotting (it increases with defense slotting) the Scrapper version is usually pegged to 95% no matter how you slot your defenses. The stalker one can get to 95%, but it usually requires making sure you aggressively slot all defenses.
Conversely, stalker SR has higher defenses and significantly higher AoE defense. First, for melee and ranged defense SR's powers have the same defense for scrappers and stalkers, but stalkers have hide. 1.875% defense from Hide is immune to suppression and for SR-levels of defense that can be significant. +56% defense slotting equals 30.4% defense for scrappers, and 33.35% defense for stalkers. On top of that, stalker Evasion is stronger (in defense) than scrapper Evasion + Lucky: base 21.375%. So +56% slotting for stalkers would be 36.3% defense to AoE.
So higher defense, much higher AoE defense, lower scaling resistances, sometimes lower DDR.
Also, I should point out that while Ninjitsu did not have the scaling resistances, it did have straight-up resistance to both Psionic and Toxic. That means Ninjitsu tended to be stronger against psi in particular than SR having both psi resistance and a heal verses SR only having higher defenses against positionally typed psi.