Probably half of the story, that's what's missing. You know how in previous Assassin's Creed titles, the protagonist grows along with the story and the transition is subtle. This one is the most promising title in the series, it has everything that made the previous ones great and none of their drawbacks.
The stealth, sailing, fighting, everything is great, mission variety, even the story is great. But it's too sudden. I can see it's missing a lot. And a lot of the map will remain unexplored, at the end of the game. To see everything you really have to go out of your way to see them and it's no fun because it feels pointless. Shay's story is over why explore. Also, the story is disappointing. It has great potential and great protagonist but because it's rushed, it doesn't have the same impact. Even the ending is abrupt (I really liked the ending of Black Flag, even though we know things after that didn't go well for the Kenway family, but the game ended on a high note).
Let's talk about the present day story. A total let-down, again with great potential. Again, it's not bad but it's too short and the modern story doesn't even have a any kind of twist at the end.
It's the first game of the Assassin's Creed franchise where I completed and saw everything (100%) just because the story was so short that I've invented my own reason to explore. And still, that part was boring but the locations were way way better than anything in the previous titles.