I God let Noah make a vessel to survive then his intentions were not to use a miracle... I mean... it does not make sense at all... What is actually more important to mention is the fact that the whole Genesis account has probably been written 600 BC. If it is written at that time then it is no wonder that you find a story about a tree with a serpent, a godlike (made in image of god) man and women, Nephilim and a flood since these stories can be found in other tales which we see as Myths.
Also the inconsistency of the Nephilim has always troubled me: the genesis account says this: The Nephilim 2 were on the earth in those days, and also afterward, when the sons of God came in to the daughters of man and they bore children to them.
So... the writer of the story gives us at least one reason why the flood was not at all that effective: the nephilim live after the floods as well. Also it states that the sons of God came in to the daughters of man (after the flood)! The whole reason for destroying the earth then is gone because of that sentence. "Proof (or at least the Biblical proof)" can be found later on AFTER the exodus: the Nephilim were still there and needed to be destroyed and even until the days of David there were still Nephilim. So: the flood IF it happened at a scale we read about, was not as effective as it should have been!
Now coming back to the paradox: God can do miracles and he could have easily killed the wicked persons by for example let their heart stop bleeding. He could have killed men without killing the animals etc etc etc. There is absolutely no reason why he would have used a flood for it.