I'll give it to Bethesda, somehow their sub-plots and character backgrounds are written in a very mature way. Ulfric was the definition of a great leader with greater than life personality yet he was one of the unique type of leaders for whom being selfish and being idealist was the same thing and serving the same purpose. He wasn't a great general, wasn't a legendary warrior yet he's was coming from a breed that could do great or/and terrible things by leading his people.
So i think Bethesda may come up with good background plot with synths.
While it's a valid argument that any sentient being with will to live is not different than a human being and deserves the same rights; it's also a valid argument that there is matter of struggle for existence between species. Human kind simply destroyed most of the animal life and left the rest at the brink of extinction. For example there are 20.000 lions left in the world and they're not a food source or competitor for food; they're simply irrelevant to us humans, so they're dying out.
So any sentient race introduced is also a case againts survival of humanity. Just letting them be, may lead to human extinction in the future. Because they follow a different evolution path which is far more efficent and even more rapid, only thing that is quick enough to oppose them is the speed of our technological advancement which is halted for good in Fallout universe.