While Assassin's Creed would do a lot better without the Desmond/science fiction arc, it's not a bad story.
I'd like to see a few examples of "good" stories from people constantly deriding it. AC, like many games, is pure pulp. But it's often enjoyable despite its low points.
It depends on how you approach the idea of game storytelling. It's never about how complex or stuffed you can make something, it's what you do with the medium that makes it interesting.
To me, almost all game stories are awful. But there are two types that seem to break the trend, and I can separate them by their flagship examples:
1.
Planescape Torment - Extremely dense and superbly well plotted top-of-the-class story that sacrifices gameplay quality in the name of storytelling cohesiveness. In games like this, the storytelling might be experimental or
avant-garde, or it might be straightforward but extremely dense and detailed and, generally, written by someone with talent in the field. These games frequently have gameplay which may be an 'afterthought', but stories which pick up the slack for their underwhelming mechanics. These are rare games indeed, I can only list like maybe six-to-ten that really do the story well enough to make up for their gameplay shortcomings.
2.
Shadow of the Colossus - These titles take the opposite approach: vague or interpretive storylines which use the medium of gaming to impose emotions on the player that allow an open dialogue with the characters or events taking place. These titles usually utilize the advantages of the gaming medium - like forcing the player to participate in the brutal murder of seemingly gentle colossus' - to make the player comprehend the scenario at hand, rather than long passages of writing by talented folk. They also often have low frequency of dialogue, in favor of character emoting (say, the way Link does in Wind Waker) or specialized events which cause a player to consider his/her actions.
Titles like Assassin's Creed, at least to me, fall in some no man's land that doesn't do anything well at all with regards to storytelling, unless you're talking about extremely specific moments. They're poorly plotted, frequently non-cohesive and convoluted, and they use the medium of gaming terribly as it relates to the advantages of storytelling.
I want to say that I believe part of the problem is this whole MAKE A GAME, EXPECT A TRILOGY nonsense these days. Every game series has to be a trilogy, and because of that plotting and planning becomes infinitely more complex over the six-to-ten years it might take to release all three games. Staff changes, leaves... it's extremely hard to be consistent about storytelling in such an environment.
But part of it is just lousy writing altogether and a poor emphasis on integrating storytelling in a way that makes sense for gaming.