They should add the Abstergo parts back into the game as an option that you can turn on.

I recently had a discussion with a coworker who's a lot younger than me and just never played the original black flag and didn't know how it fit into the story of the other games. Now I will readily admit that its not tightly connected, but it would be nice to have. If they start stripping the modern day elements out of the other ones as they remake them we are going to have a lot of confused new player I think.