if they wanted to have a reboot they should have done it the right way. like the Fullmetal Alchemist animes were. they are very similar all the characters act the same, it manages to introduce new characters all the history is the same and that's what I think is important.
I dont feel like that's the right example as FMA wasn't a reboot. The author requested that they ended the story differently than the manga and they followed suit.
A better example would be the batman movies.
When it comes to plotholes, I really dont feel there is that much plotholes that you need answered. Last time I checked this series was still easier to understand than Kingdom hearts and is nowhere as complicated as Marvel or DC.
Plus I dont think approaching things like a textbook works because you should only answer the plot holes that are relevant to the story.
Answering how Nero is related to Dante is more important than giving a reason why Dante's amulet changed colors between 3 and 1.
The only questions you really need to answer are-
is vergil dead?
How is nero related to Dante?
Why did he gets so down between 4 and 2?
Giving a concrete timeline with actual ages would help gain fan sympathy. Figuring out which of the two prequels actually happened would help. Giving more background on certain characters like trish isn't really necessary and left to discretion of the maker.
The only excuse is lack of knowledge which doesnt hold water as you have access to the internet. All 4 games are on youtube, the anime is on hulu, plus the manga and the books are still in circulation. You also have the wiki and forums like this one to give you info. I created a thread that asked about plot holes and i got a list from Lord of Darkness giving me 17 examples and more.
I've even seen fans do a better job of answering plot holes which puts capcom to shame.
So its not the titanic, its not even a disaster. Its just a half-assed book report some one did by reading off the back of the book instead of actually reading it.