Everything will back to my big theory.
The story of V should be the main story, but they never finish it, which cause the absent of V.
They are very hard to finish the main story, which barely say nothing.
I believe there was a story line about Arasaka internal conflict, which will change Yorinobu to a friend. It should be a rail story after chip quest until the divel-ending we get now, but we know and help Yorinobu in the end.
That give V a much safty enviroment. No Arasaka ninjia, can walk under the sun, and everyone knows that he is the guy who killed Saburo and got forgiveness from Arasaka, that's why everyone trust he is good and give him jobs.
To Evelyn, I think that will be a good reason for her to back to work.
Remember Hellman is close to Hanako at devil-ending, too close, it make me think if he was be designed to run after Hanako fade into shadow.
That's why Yorinobu still can't fix Relic, and V's story will happened since that time.
But they cut everything
There is quite a lot of NPC dialogue all through the game hinting at another big corporate war.