I think that Phineas guy is Sparda is disguise...
Mundus kills Eva, but spares Sparda. Sparda loses his powers and skills and is forced to live in Limbo.
Mundus wants to see Sparda suffering. So, he sends his forces to hunt Sparda/Phineas wherever he is ( note that Lilith says that Hunters once found Sparda, in that introduction video).
Knowing about his, he decides to assume a new form ( Phineas) so he can get rid of his pursuers. Still, they find him and try to damage him. Dante helps and Phineas says he needs his eye back.
So, we basically have the idea of Dante helping his own father, without knowing that he is indeed his own father. Phineas/Sparda knows that it's dangerous revealing himself to Dante, after everything that happened. Think about it, it's common sense. It's not something to risk, Phineas just says what Dante needs to know.
Sparda knows he isn't able to fight Mundus personally, but he knows Mundus weak point and how he may get eventually defeated. Limbo and Mundus actions ( taking Phineas powers) prevent him to do anything to help Dante. So, the only way to help him, is making a good use of words.
He knows that Lilith is expecting Mundus child, he knows about Nephilim, he knows about DT. It's up to Dante follow his father's instructions.
During the ending of the game, as soon as Mundus is defeated ( or killed, I'm not sure), Limbo gets destroyed and every damned soul or entity ( which includes Phineas) is free now. So, Phineas/Sparda has all his complete powers back, BUT he still doesn't reveal himself as being Sparda.
He vanishes and while Dante is walking away, we can hear someone talking "Thank you, my son". So, we can assume that it was Sparda talking to Dante, but without revealing himself as being Phineas. Only the major audicence ( us, players) will know he was indeed Sparda and that he chooses to keep his true form hidden, in order to avoid putting Dante in danger. Sparda knows he won't be able to stay with Dante. After all, the demons probably should still be out there.
So, Phineas will probably check Dante's action, from distance. Anyway, it's a theory and they could really pull us a Keyser Soze a la The Usual Suspects.