The flood happened precisely on account of the issues you raise. More specifically, it debunks the premises on which those issues are founded.
As Christians living thousands of years later with only a short Scriptural account to go on, we can really only speculate about how the people of Noah's day must have reasoned with themselves. However it seems likely based on their recorded reactions and God's action that their presuppositions were similar to the ones you have made. They were wrong and the flood was God's way of setting the record straight.
There is no such thing as "probably innocent". The fallen nature of all humans since Adam means that we are guilty and deserving of condemnation from the womb on. That God could wipe out all humanity in the way he did helps us understands God's disposition towards sin and gives us a reference point for man's sinful nature. The NT echoes this as it affirms that there are NONE righteous on their own apart from God's intervention. The pre-flood people of earth are used as a reminder of this and the flood stands of a warning of the future judgement we will all face.
It wasn't God's mistake in the first place that he would need to "fix his error". The error lies with man - who chose to rebel rather than obey - but the solution cannot come from man, it must be directed by God. It was God that preserved Noah. It is God that will preserve some men (those who by faith in Him come under his saving grace).
God didn't mess up that would need to start over, it was always his plan to redeem creation. He knew what would happen to it, but entered into a covenant with himself - God the Son agreeing to be the ransom, the redeemer to purchase a people out from God the Father's righteously judgement. The concept of redemption was always part of the plan. Likewise we look forward to a new heavens and a new earth -- not a different creation entirely but a re-creation -- a redemption of creation itself on the day where he will make all things new (after he finally judges those who do not have faith in him).
Other species are not innocent. All of creation was subjected to the fall. The caretaker of creation - the priest who's job it was to mediate between God and creation - the one who was charged with naming and caring for all the species - fell down on the job. He left his job unfinished. As a result of his failure, not only was he himself cursed but everything in his domain was cursed as well. The ground brought forth weeds and thorns. The animal kingdom was subjected to the same futility that mankind was now under.
The exact "why" if many of God's choices is not fully revealed to us, but Christians use God's actions in the past to help shape their understanding of the present. The flood helps reset our understanding of what guilt and innocence mean in relation to a holy God. It teaches us significant lessons about the nature of man, creation and God himself. It warns us against evil and points us toward salvation.