We can start with the one's you brought up
Did you not tell me once that you could get all our current genetic diversity out of a few species on the ark or some such thing ? This would be a good explanation were it possible .. but its not - unless you invoke magic .. aka - direct intervention of God .. to speed up the mutation process .. which didn't happen .. as we would see it in the genetic database.
Then there is the problem of how to get those animals back to their original locations .. and leave zero traces behind. Magic
The one that I like to focus on though because the Magic God/Satan - or whomever think did it - would be way off the charts.
The Flood is dated Biblically to around 2100-2300 BC .. Abraham was around roughly 1800BC .. Flood happened 300 years earlier according to the Bible. The problem with this idea is we have continuous civilizations throughout this time period .. none of them just Stop .. even in the dark age periods .. when the timeline resumes it is the same culture .. and not a different one .. and this is a huge problem .. unless one wishes to claim that God planted all the evidence .. archaeology, history .. and no fancy dating methods required .. its just history .. this is not that far back.. and archaeology backs up the history - and creates some of it as we an read texts from 1800 BC .. and we are finding more all the time from 1000-1800 BC .. There was no Global Flood round 2100 -2300 that wiped out all land creatures.
Now . perhaps there is a literalist way to argue that what is being referred to is a more local rather than Global Flood ..as to the story teller - passed down through oral history it was a global flood. So to these folks - there literally was a global flood .. but their literal and your literal are two different things.
There was a massive flood around 5000 BC in the near east when the black sea was created. You could easily have a small group of people on some makeshift raft be the only ones to survive .. and never see another person again.. during their lifetime.