It seems to be the Lost Number. Here's why:
Beyond the door that no key can open,
It is within the safe in the Shinra Mansion in Nibelheim, and a safe has a door which no key can open (at least not all safes have a key or a keyhole).
The rejected one lies in wait.
It is largely implied that the Lost Number is a rejected experiment.
Two faces has he,
A creature with two faces, or more correctly, two different sides.
One of power and one of wisdom.
Power refers to physical attacks while wisdom refers to magical attacks. (This analogy I agree with.)
Yet if you possess the courage to face him,
It is an optional side Boss you can fight.
He may show the way to a great secret.
The great secret that is referred to here is likely to be Vincent.
Can you tell me of whom I speak?
Lost Number.
PS: Forgot to mention that by 'show the way' in the second to last line, it refers to the key for unlocking the door to the room (or is it the hidden door to the basement, can't recall) that let's you get Vincent.
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