Story and plot are not the same thing. I think the reason you get these kinds of stories is because video games in their current state lend themselves to this kind of storytelling.
But can you name one story in history, outside of poetry or allegory, that can't be descried as "A bunch of people do shit"?. Some might say that it isn't the plot that makes these stories great, but I think trying to separate plot and characters is pointless.
When a character has a personal revelation it's a plot point. When a relationship begins or ends, it's a plot point. When a character is given the opportunity for revenge, it's a plot point.
What you're describing isn't simplicity of story, it's simplicity of structure. It dictates less than half of a story, there's still context, theme, tone, setting, and all the character interaction.
As long as they are, it's just easier to develop games this way. You use a familiar archetype and write a meaningful story around it, so events that would normally seem by the numbers have emotional and thematic weight. The most original plot in the world won't save story from a generic uni-dimensional cast, or a flat uninspired tone, or a fractured sense of pacing, or a lack of thematic depth.
Assassin's Creed(IMO) has these problems, the later one's in particular. Sure, the plot is relatively novel, but it doesn't feel any different because that's all it is. It's new, but it doesn't MEAN anything.
The characters are generic, uni-dimensional and morally black and white(Despite being in reverse, which I think is kind of ironic), so it's impossible to get emotionally involved because you don't care what happens to them or why.
The first game kind of had a nice Orwellian feel to it, but later installments dropped all the bleakness and felt like The Da Vinci code populated by the cast of Scooby Doo.
The series has always felt thematically dead to me. The struggle is black and white, the Templars are evil because they just are, the Assassins are good because they just are, and we're fighting to save the world because we couldn't think of anything human to motivate us. Neither of the binary sides of this equation represent any kind of complex ideal, nor does the struggle itself have any dramatic weight. Why?, because one side is trying to save the world, and the other side is fighting because they're greedy, or aren't given any reason at all(Presumably because they're going to try and paint them sympathetic later). These are things that almost anyone would fight for, so they're things we've already figured out and they don't tell us shit about ourselves or anything else.
WHAT happens might be interesting, but we don't care about how or why because those parts of the story are so binary.
Mass Effect's SUMMERY is pretty paint by numbers, but we care about what happens because the conclusion has consequences we can relate to and invest in. A single aspect of a story can be forgiven if what surrounds it is exceptional, but a mediocre story cannot be forgiven based on a single novel idea.