The true ending is actually pretty depressing, Whether you like it or not, It'll happen.
I don't like it either but..
Don't listen to the conspiracy theories. People think that the Aya in the vat at the end is the real Aya or that Aya is a good person running the clinic.
The Aya's were not switched. In the true ending, Ogre (the red eyed stranger, just like the book on Aya's shelf) brought Alfred (the father) back from the dead and into another dimension. that's why his hair and hands are purple. Ogre said "Maybe one day you can show this girl your homeland". That means that the Aya in the glass (who is quite curvaceous for an 11 y/o) has never been in the real world, meaning she was never the real Aya, and is a recreation made my Alfred to fulfill his desires.
And as for the theories about Aya actually being a good person at the end... oh I wish I was that naive... It may look that way, because Aya is helping Jean at the end and Maria said she is just like her father, so some people t