Oops I stopped reading the list like halfway through but also 40 is one I'd be immensely interested in hearing your answer to.
What’s that? How would I fix Crisis Core? Wow you caught me completely off-guard on this subject I clearly have never thought about before, guess you’ll have to bear with me!
Prequels in general should contribute context and understanding rather than just a series of things that happened, and Crisis Core did not do that. It wasn’t very good at being about anything, when it should have been pretty clearly about one thing: Shinra is terrible, and working for them is a spiritually and morally corrosive experience, regardless of how apparently decent you are as an individual.
In VII we see Shinra kick a puppy every couple hours, but their real bone-chilling atrocities all stem from a complete disregard for life beyond that which is exploitable. Their real damage is expressed through the characters we meet that they have destroyed. A prequel’s the perfect place to look at that in greater depth, and from the inside.