The reason he sounds young is because, in a lot of ways, he is. He was about 25 physically when the Nibelheim Incident occurred (according to my calculations, anyway - Nibelheim happened 5 years before game canon, and according to most sources, Sephiroth was 30 at the time of the game), and I tend to put Nesa as being about 5 years older than him (so she's about thirty at this point). Socially, he's maybe half that, if not less - it depends what age he started fighting in the war in Wutai. As far as I can tell, there's no canon mention, so I tend to put him at about age thirteen or fourteen when that happened. This means his "social age" is about twelve or thirteen years at most. It's helped by a rather limited set of circumstances which mean he doesn't have to acclimatise to the full range of human social interactions, but even so, he's not even as socially adept as (for example) Cloud Strife.
As for his emotional age, which is what Nesa's largely dealing with in this context, that's even younger still. Emotionally, he's maybe about four or five, if that.
The bit where he calls Nesa his "mother" is because he reasoned it all out logically - she's doing a lot of the behaviours she's attributing to a mother (in the social sense) and she's the right gender, so she's obviously his mother. The fact that it's one of those things which *isn't* logical, and which she's going to have to explain in social context, is one of the reasons she's busy hiding behind my hindbrain and having a breakdown.