Nagato died at the age of 35, and Kushina, at the age of 24. Naruto was 16 at the time of facing Pain, so Kushina would have been 40 had she survived, meaning she is 5 years older than Nagato. If we assume Kushina was brought to the Leaf around the age of 8-10 to become the 9 Tails Jinchuuriki, Nagato would then be 3-5 at this time.
Nagato, living in an isolated area in a war-torn nation, would be less likely to attract attention with his Rinnegan than if it were discovered in the Leaf (Danzo would have a field day with that). Also, that type of environment would make Nagato more easily manipulated to follow Madara's ideology.