Depending on how you read it, between Yahweh deciding to flood the world, and actually doing it, there were between 7 days and 100 years. Probably lots more than 7: that was the time Noah had to load the ark itself, so construction would've begun a while before that. A few months to a year, let's say, between Yahweh deciding "kill everything" and actually doing it. Let's call it the time between P-day (when he made the plan) and D-Day (when he started the rains).
Here's the point: it presumes that Yahweh knew on P-Day that everyone who would be alive on P-Day (except Noah et al) would be evil and deserved to die. It's that, I think, that gives the most issues with free will....and god's benevolence.
On free will.....once P-day had passed, nobody could make any other choice than to be bad, without cauding god to explode in a paradox. There is even, perhaps, an argument to say that once god made his mind up, he CAUSED everyone to head towards evil from that point onwards. The omniscience vs. free will argument comes up a lot, but its this period that hihglights it most strongly, I think. Equally, once god decided they would be saved.....did Noah and crew have the free will to be able to sin?
On benevolence......But if we assume that men COULD still make a free choice....then does that not call god's benevolence into question? If it were still possible for a sinner to be redeemed, then does not P-day make him evil himself? In the gap between P-day and D-day, a man with free will could have turned to good (perhaps swayed by Noah's example). But it was clear on P-Day that god had decided to save only Noah and his family - so everyone else, from that day on, was stuffed. No matter how good they bacame in those few weeks and months, they were already doomed.
So to me, that period of time, above any other part of the Bible, highlights how horrific Yahweh actually is - he either damns people be setting the future, or damns people by not caring about their actions.