Noah's Ark - Miracles?

Some would answer all my questions about the difficulties of Noah's Ark by saying "Well, God simply cared for everything miraculously." If that could be done, of course, there is no need for the Ark at all. God could enclose every creature and plant in magical bubbles, putting them in stasis during the flood and restoring them afterwards. For that matter, why even bother with the flood? Just instantly dispose of all the evil or non-believing humans and start over with Noah's family. Saves lots of hassle. The trouble with miracles is, if they are so easy for an omnipotent God, why mess with non-miracles? Ah, but the stock response is "We cannot know God's reasons, ways, and motivations." Hmm, there certainly seem to be a lot of people in the world who claim to have hotlines from God with rules that they are more than willing to impose upon others. They assert the literal truth of scripture (do they really know what "literal" means?), but at the same time insist that their personal interpretation of scripture is what counts. "Scripture doesn't mean what you say, it means what I say!". I love fantasy literature, and the Ark story is just too good to ignore; I just want to understand the details of the cruise.