I agree. It lacks as much weight when I simply see both of little Jona'Hazt's parents talking about him while being killed by geth, instead of watching he himself get blown apart into red mist or suffocated just the same by the toasters. How about some Krogan Rebellion era archive footage of salarian/turian/asari kids literally being eaten, eviscerated or evaporated in asteroid strikes by the hyperviolent battletoads? Reapers tossing some kids and infants that can't be used as husks into a protein vat? Wonder how many less would have cured the genophage/saved the geth/ chose synthesis with such things present to provide a more fair and balanced treatment of those options?
Didn't you know? The Krogan and Geth are blameless, holy creatures set upon by a cruel and heartless galaxy. And the Reapers, well they are just mindless forces of nature, like fire. But yeah, it was really annoying to see all that revisionist history/whitewashing at work for the Genophage and Rannoch arcs. Forget the redirected asteroids on Turian garden worlds, forget the near extinction of the Quarian species, forget the Reapers' (Harbinger's in particular) sadistic pleasure from liquifying colonists slowly, one at a time, in full view of each other, etc. Just go along with the narrative slant. 
As you alluded to, Dead Space did this right. Kids don't get spared of the horrors of mutilation and calculated genocide by virtue of being innocent according to our systems of morality. Perhaps they needn't make it as graphic because ME isn't primarily a horror series, but children only being mentioned in dialogue yet never visually breaks immersion and immediately calls attention to how sanitized the subject matter of the setting is, all for the sake of most players being able to enjoy the good feelz and consequences of some of the rather reprehensible actions they are allowed.
Exactly, you can't have it both ways (IMO).
You can't present a setting as dangerous and capable of doing horrific things to people, and yet have children present who are exempt for any and all collateral damage. Either you have a setting that is equal opportunity in terms of potential violence, or you have a setting where violence is a nonexistent element. Trying to force the two together creates a narrative disconnect.