In an interview with The Official Xbox Magazine, Assassin Creed III's 'mission director', Phillipe Bergeron, explained that Ubisoft initially had plans for a 'huge' co-op element in the original game, but that the idea was dropped:
“Before we knew about the Desmond story and Animus link, we had a huge co-op component in there. But it just became too hard to do: the engine couldn’t support it, and then the metaphor we had above it didn’t support it.
“Co-op was one of those big things at the beginning that just didn’t make sense in the end. For us it was really part of the single player experience, to have in-and-out co-op, and in the end we never thought it made sense in the storyline that we had for the Animus.
“There was no way to reconcile having multiplayer or co-op in an ancestor’s memories. Your ancestor lived his life in a certain way, so assuming you had branching storylines, it creates a paradox. It didn’t fit.”
So one reason is that the engine couldn't support it, the other is that it also couldn't be reconciled with the story anyway. Presumably the engine in Assassin's Creed IV (come on, we all know it'll happen) will be powerful enough, so the question is whether the inability to work it into the story will take a back seat to the desire to introduce a co-op mode. Hmm, I wonder...