Theory time
We know that Angus found the Yamato but broken .. well .. (here i go XD)
Could Nero be a remenent of Dante and Virgil?
Angus was a scientist , it says he recently started researching demons ...
The Order could have took DNA of the Yamato which would contain the blood of Virgil (when he cut his hand for the ritual) and Dante (when Virgil impaled him) and fused them together to create Nero , A rememnent of Sparda. That would explain why Nero has Sparda's blood and acts like Virgil and Dante and also explain the pre-mature Devil Trigger!
As Nero was growing up , the order could have thought that they could not wait and searched for Dante , so untill Sanctus saw his fighting abilitiy , he saw his perfection. Angus and Sanctus could have been hiding the whole thing , as when Angus stutters in the opening saying "that kid posesess d-d-d-demonic power!" , Credo was there ...
hmm ... Not close I think but its a try.