Who is Phineas and Candace's biological father? Who is Ferb's biological mother?
Despite all the fan speculation, this will likely never be revealed. Just like the nature of the relationships ending (divorce, etc.), this is a subject that is probably too deep to be answered. It is, after all, a cartoon. Don't think too hard about this.
Why does Doofenshmirtz hate Perry?
He claims that Perry is his nemesis, but Perry and the evil doctor have a bit of a love-hate relationship. Doofenshmirtz has been visibly upset when Perry has not shown up to defeat him. Perry, on the other hand, was heartbroken when he was replaced by Peter the Panda.It could also be theorized that Perry's and Doofenshmirtz's rivalry could just be "work related" in essence, as a few episodes have shown them facing each other, when Perry is not on a mission, and no battles take place.
He's a platypus. They don't do much.