The ending that I was hoping/expecting (spoiler)
I wasn't surprised that Will had survived in that shelter in his home, after all, the beginning foreshadowed that quite directly.
However, since Will was able to recreate a body identical to his, why didn't he upload his mind to a recreated brain? I suppose this could go beyond his capacities. From a science-fiction point of view, the idea of going from AI to organic intelligence would have been an amazing way of avoiding that virus and, in essence, creating a biological back-up. Perhaps that intelligence would have been more limited, but he could have tried to recreate the original Will, i.e. the intelligence the AI started up as.
Perhaps Will should have tried avoiding human detection for many more years/decades until he figured out ways to be essentially indestructible. For instance, he could have created more ways to exist "offline".