Amnesty International documented more than 30 attacks in eight months.
An African Union peace roadmap could help resolve three deadly conflicts in the country.
Darfur will remain as five separate states rather than uniting into a single region.
Human Rights Watch called on Sudan's government to disband the Rapid Support Forces.
Yet President Salva Kiir told regional African leaders at the ceremony that he still had "serious reservations."
The EU has already made clear it rejects the legitimacy of the elections.
The South Sudan Democratic Army (SSDA) Cobra Faction has released 1,314 children since January.
The request comes weeks after allegations of a mass rape by Sudanese government forces.