What are you missing?
Quite a bit, actually. First, you have no idea how wicked and degenerate people had become in the days of Noah. According to one extrabiblical account, Enoch beheld the Lord weeping and asked, "How can you, the great God of Heaven weep?" The he was shown the flood in vision prior to its happening. Like Abraham, he reasoned with the Lord and sought the Lord that he should turn away his anger. But then the Lord showed Enoch the people themselves, what was in their hearts and what went on in secret. After that, Enoch was wroth with the wickedness he saw and in essence said, "You should wipe them from the earth!"
Things aren't always as they appear in polite society. It's difficult to imagine intelligent beings burning and sacrificing their own infants to idols and giving way to gluttony, bebauched sexual practices and practicing the basest villiany possible to the point that they're beyond any hope of repentance. The legend of the flood is one that is had among all the nations of the earth, and it represented the baptism of the earth by water. Armageddon is the battle that will take place just before Jesus returns to the earth with fire, representing the baptism of the earth by fire and the Holy Spirit. Even so, the Lord will spare one-sixth of the enemy troops because they lacked complicity in the attack of Jerusalem.
One professor of theology I know was one time the Number 3 man in the FBI. While in that post he was struggling with how the Lord could destroy an entire people. He told me that one night he was having dinner with some friends when there was a knock at the front door. It was several FBI agents with a critical matter that required his attention. He joined them in an adjoining room and was subjected to details, photos and testimony that made him so physically sick that he went into the bathroom and threw up. That night, on returning home, he wrote the segment covering the flood and man's ability to resort to the most disgusting and sickening behavior in the books he was writing on the Old Testament. Over the years, he's never forgotten that night and the effect that paperwork had on him.
It's easy to second guess God, but it's not generally a good idea in my book. This doesn't mean God didn't love the people He destroyed; they are His children, just as we are. But they didn't cease from being. Instead, when their bodies died, they were put in sort of a penalty box, where they stayed until the crucifixion of Jesus. Peter writes:
For Christ also hath once suffered for sins, the just for the unjust, that he might bring us to God, being put to death in the flesh, but made alive in the spirit: By which also he went and preached unto the spirits in prison, which sometime were disobedient when once the longsuffering of God waited in the days of Noah, while the ark was a preparing, wherein few, that is, eight souls were saved by water. (1 Peter 3:18-20)
He later explained: " For for this cause was the gospel preached also to them that are dead, that they might be judged according to men in the flesh, but live according to God in the spirit. (1 Peter 4:6) In other words, they will be judged as men in the flesh even though they live as spirits. The prison corresponded also to "Paradise" (a place of rest, or more precisely, a place of "the king's rest"). Thus the thief on the cross also became one of those who was preached to.
Not all were equally as wicked in Noah's day, but my point is the God "wipes out" no one. He just...ummm...changes their scenery. Even those destroyed at Jesus' coming will be very much alive in spirit. And though they may be punished, it will not be forever. Some believe that Hell is both temporary and remedial. And ultimately men will be their own tormentors.
(P.S. -- The "nephilum" is a fanciful story and did not refer to angels at all. This issue of "giants" is an interesting topic and one for another topic.)
