The reality is that other than the day Jesus was crucified, this was earth's darkest day. There was nothing cute or pleasant about it. Pretty much every living thing on earth was destroyed. I guarantee you even the mood on the ark was dark. God's justice and power was unleashed on this planet in a terrible way. Humans had become so evil, that basically God felt he needed to "reboot" creation.
It's also a strong reminder that another day of judgment is coming. The Bible teaches us that there will be another "reboot". There will be a new heaven and new earth. Those who are following Jesus Christ, will receive an eternal reward complete with a new body and a new name. Those who have rejected the gospel, will receive eternal punishment.
Rather than turning this story into a cute children's "fairy tale", we should remind ourselves of it and learn from it.