I have no issue with the idea that God, as creator of the universe and giver of life, has the authority to take it back as He pleases. I take no account of any bugs I might step on when I am walking outside, and we are far less than that to a being capable of creating a universe that is farther across than we can comprehend. And as an all-present and all-knowing being, He also does not suffer from the flaw of human-imposed punishment: He always knows for certain that someone is guilty of an act or not.
Thus, I interpret His actions in that context. And it makes God unpredictable. I cannot imagine that every single human person (with the exception of Noah and his family) in the world at that time was so wicked and so depraved as to deserve death. And it seems unnecessarily excessive to also destroy so many animals as a form of collateral damage. Based on my explanation above, God is within His rights to do so. But that doesn't strike me as just or merciful. It seems more rash and cruel. This is the same God who wishes for all people to attain salvation, but at one time he wiped out almost everyone and everything.
Now, this could be wrong. If every person had fallen to such a degree that all of humanity (minus eight people) were irredeemable, we can say that God was being just. But that means that not only had mankind fallen from perfection right from the start, but that their condition deteriorated so completely within a few (hundred? thousand?) years that God had to effectively start over. And the reset did not work very well, either. Noah got drunk, his son was cursed for looking upon his nudity, and before long humanity seemed no better off and required yet another intervention (this time it was language, and that change did not seem to help either).
Genesis sometimes seems like a record of God's plans that went poorly. The notion that He did so from incompetence is not reasonable, in my mind. Thus, this must be deliberate. That is the sort of God that would make me very scared if I believed He were real.