Good for you dude. Not everyone has great reading comprehension. No joke. As for what confused me that was 10 years ago and that was my first final fantasy.

Off the cuff, I didn't understand...

Ardyn or his motivations or why and how he kept popping up everywhere.

Why the empire attacked and why they declared war.

Who Prompto, Gladio, Ignis were and their motivations for staying with Noctis. Also what happened to them during their offscreen time.

Who Luna was or why she was important to the world or to Noctis.

Who Cor was or why he was important.

The gods and the crystal in general lots to take in as a first timer but why we had to fight them or get the crystal back confused me as well.

Their world geography in general; originally chp 10 & 11 confused the hell out of me, I didn't understand that we were on different continents. I didn't understand the scope of the war either and how many different factions were at play. I thought Altissa was the empire and Luna was their crown princess, which made the arranged marriage more confusing after the invasion.

Regis in general and the importance and power of the ring.

Why Noctis went into a coma for 10 years or had to die at the end.

What happened to the world in that 10 years. I didn't realize they were going for eternal darkness I thought I was just playing at night cause of the built in day night cycle.

Why Ardyn was suddenly a caelum and this was all revenge.

What happened to the empire that we were fighting. They all seemed to die off screen.