I think that there are many things that should be taken into consideration under the theory that Viola is Amy. I would like to mention that although Raphael had managed to become infected with the essence of Soul Edge, Amy, as far as we know, only managed to come into contact with Raphael's infected blood upon her bare flesh opposed to it infecting her blood stream.
I don't really know how that may affect her in turn, but I think it's very possible that Soul Edge's influence had managed to make the pigmentation in both her skin and her hair moderately lighter as time progressed. Since it's never been confirmed that she has vampire traits similar to what Raphael does, only fan speculations, I think that she most certainly has not been separated from the aging process; but perhaps, it has been slowed down considerably?
Some speculate that if Viola was Amy, Raphael would have noticed her relatively quickly. From what we gather from the story, Raphael has no recollection of what had occurred prior to being locked away within a holding cell, so it's possible that he had been unconscious for the 17 whole years leading up to Soul Calibur V. He also seems to remember things that occurred before he was unconscious, so he may not even be aware that so much time had passed. It could have felt like he just awoke from a short dream, for example.
If we assume Viola is Amy, there would be plenty of physical differences:
1.) She lost the childish 'chubbiness' in her cheeks in favour of a more toned, mature appearance.
2.) Her hairstyle and hair colour remained elegant, but became more suitable towards one of her age.
3.) She had naturally grown taller and began to mature into a young woman; whilst some features aren't as elaborate as some of the other characters, she had most certainly began to go through the stages of puberty.
Not only that, but Raphael would more than likely be in a state of panic and confusion at everything he encountered mixed in with his want to find his beloved daughter. Viola speaks in riddles and appears as a cold, uncaring woman; Raphael would possibly be used to Amy showing at least some form of affection towards him. Basically, Viola and Amy would have practically very different personalities towards him.
That always brought another question to mind, though. I wanted to know how or why Amy would have gotten powers like that; so, I did a little research.
Viola's Critical Edge is entitled "Arcanum Azarael". Directly translated, the result would translate to "The Secret Of Azarael"; an interesting fact is that in religious mythology, Azrael (rarely credited as Azarael) is known as the archangel of death who is an embodiment of evil.
I think that it's a very interesting relation corresponding to Viola's character and her background, especially when taking into account her special abilities. Upon using her Critical Edge, she channels her magic into her crystal orb which in turn slowly pulls the enemy towards it; I think that makes a fantastic metaphorical representation that death is unavoidable and is constantly pulling those who live into it's dark embrace, no matter how they try and avoid it. Considering Viola's power of being able to see into people's future, regardless of whether or not she speaks to them about false states of happiness and truth, it's an interesting concept to think that she could be considered as a messenger of death that judges all that roam the earth.
The heavy burden of understanding what the purpose of life to a certain individual would be, for example, would weigh constantly against her own shoulders. Especially since she finds it difficult to see into her own soul.
Since Soul Calibur has a series of implementing historical and religious context into the story, could it be possible Viola may have gained her powers from something/someone like that? Does anybody have any thoughts?