Black Flag is the standard. Its mostly standalone in terms of story, by which i mean that even though there's a lot of references to past games, the information can be soaked up rather easily and filtered. In terms of gameplay, it is one of the most versatile in the franchise (from the ones i played).

Assassins creed 2 is a good one for story, but for the best experience imo, you'd need to continue on to Brotherhood and Revelations. Assassin Creed 1 is ok, but not entirely needed and Assassins Creed 3 is sort of an ending to the story, but it's not as good.

For any others, I either played only a bit or didn't play at all, so I can't say much except that they aren't fully tied to the original games in terms of story.