There will be some explanation or a cutscene in the future, I'm sure. If they did not want to use Vergil at all, they wouldn't include Yamato. The thing is, Nero keeping the Yamato or say inherit it from Dante, is a kind of gravestone for Vergil's return in full form. That's why I've said that a possession of Nero by Vergil could be likelyin the future. Especially the key point for me is the phrase '' Power....." which Nero heard when Yamato reacted to his Devil arm. There's something there..

... And she cradles me down into sleep
Still I miss her so and for more I weep
And she gives me death yet i'm alive
raving eternally, on her I thrive..
... And she buries me down far too deep
Yet six-feet high and gives me bliss to keep
and she abuses me yet I abide
She's in demand, my hunger I cannot hide..
Her name's Jez..