It's an interesting read, but some of the plot holes aren't even plot holes, and they even explain how they could happen. I'm thinking specifically of the ones for IV and VI. Some others they think are plot holes but are really just them trying to apply gameplay logic to the story which is a bad idea in pretty much every RPG ever made. Sure in FFVIII you know that you're party might be powerhouses who could take on an endless army of enemy troops, but if the story assumed that then the whole game would be pretty boring. We know that there's nothing in the game that will actually beat you, but it's hard to build dramatic tension if you just assume all of the characters are godly.

The list of goofs are a little better if you ask me as they are generally goofs whereas the plot holes are a little iffy.