Hmm...Old Testament morality issues...a toughie indeed.
Ah, I have just the book for you (starting to feel like Twilight Sparkle saying this). The answer to every one of your observations can be found in it. It's When Critics Ask: A Popular Handbook on Bible Difficulties by Norman Geisler and Thomas Howe.
I went ahead and looked up some of your inquiries and have provided the answers to supplement my knowledge. I didn't look up all of them, as the book is 604 pages long.
-I almost didn't have to look this one up. When God flooded the earth, destroying a creation He earlier considered "very good" and then one He declares "He is sorry that He had made man on the earth," (Gen 6:6) He is obviously destroying an earth that is beyond salvation- one so evil that no man can save it. Had He left the earth it as it was, it would have been a terrible, miserable, empty, futile place. (Geisler and Howe 41)
-When God slew the firstborn of the Egyptians, he slew the firstborn of the guilty Egyptians. The Egyptian people were not in fact innocent and in fact, "a mixed multitude went up with them [the Israelites] also" (Ex 12:38). As a result, the Egyptian people knew that the God of Israel was actively judging them for enslaving His people and only the people who maintained their iron grip of oppression on the Israelites had their firstborn slain. They also could have changed Pharaoh's mind, despite his position of dictatorship via a revolution- after all, the plagues whatnot God brought upon the Egyptians made them urge "the people, that they might send them out of the land in haste" (Ex 12:33). The Egyptian people could have done something about their leader's decision, but they did not (74-75).
-(The answer to this one can be found just by reading Genesis 19). Lot's wife was transformed into a pillar of salt because she directly disobeyed God's direct order (which was delivered via two angels who spoke to Lot and his family- Genesis 19:17) not to look back at the city. No ifs ands ors or buts here- God was completely clear in His instructions and the consequences of disobeying. Curiosity and annoyance as exceptions were not in the fine print of God's orders. It's like being given the order not to look down the barrel of a loaded gun and pull the trigger but doing so out of curiosity.
I could continue but, as I said, there is an answer to all of your inquiries in various Biblical commentaries and whatnot. I'd answer all of your inquiries but I'd just be paraphrasing from a book or from the scriptures. It's not that I can't answer your questions, it's just that this post is 2000 characters long right here(-) We could go on and on discussing scripture but like I said before, this is a forum about My Little Pony- not about scriptural debate and whatnot.
Seriously, I'm not using an excuse to dodge your inquiries- it's rather late now and...I've given you my reasons.
Trust me, there are answers to all of your questions- just don't denounce Christians when you put them on the spot. Unlike Eli from the movie The Book of Eli, we don't all have the Bible memorized- and even if we did, even we might not be interpreting it correctly the first time we read it. It sometimes takes academic and historical research- after all, it was written 2000 years ago but is still accurate down to the word today. We're fallible and human.
Oh and one last thing- don't "Presume the Bible [or anything or anyone else] guilty until proven innocent." After all, what did the Mane Six learn after doing so to Zecora?
Goodness, I never thought I'd be using examples from My Little Pony to defend my faith.