That was the apparent plan. I've heard Brotherhood and Revelations was a result of AC3 taking too long to make and they didn't want to leave the series hanging for a couple years because god forbid gamers have to wait a few years between sequels.
And then the lead dev left ubisoft(or was forced out, I forget which), which screwed over the original plans. That and ubisoft wanting to make AC a yearly thing because $$$$$$$.
And while I like AC3(with caveats), I would have liked to see the original plan come to fruition, even if it means AC4 would have never happened.
The issue I think that crippled the AC series for a lot of people, is that they got the story structure backwards, based on the gameplay.
Here's what I mean:
So the entire premise of the AC series, is a pretty standard story, as far as things go. You have a clueless protagonist who in the present, who is caught up in events outside his control. He is forced to undergo experimental technology to uncover lost information, that only he can provide. The story then proceeds into a series of flashback sequences, to uncover the Macguffin in a sequential order, that gives the hero time to devise a plan to escape and thwart the badguys. No problem there, tons of movies have done something similar, specifically using a series of flashback scenes to convey information to the current problem in the present. It's a great method of storytelling, but the problem that the AC series ran into, as a result of this plot device, was time investment.
They left the "flashback" sequences as the primary game, and the "real events" as the transition scenes that last almost no time at all. And it's supposed to be the other way around. When using flashbacks, you're supposed to just dip into a short event, one sequence of actions, that are immediately relevant to the protagonists, current plight, which will provide insight into their current problem, allowing them to overcome it. And this is the important part, then you go back to the present day, real events, and show that flashback's impact on the current problem.
But AC didn't do that. They let you wander around for 20+ hours at a time, depending on how much ambling about you do, before taking you back to the story of Desmond. But the problem is that you have no investment in Desmond, because they don't actually establish him as the important person. He is relegated to a plot device, and he is the actual protagonist of the game. Because nothing that is going on in the actual game itself (the flashbacks) matters. You don't "win the day against the Templars" by doing what Ezio does, because in the present day, the Templar's still won. They control the world. So it makes all the efforts of Desmond's ancestors effectively pointless, because it always ends with the same conclusion "And then the Templar took over everything and brought the world to the brink of destruction." Nothing you do in the flashback (the majority of the game) changes that outcome. All it does, is inform Desmond on what HE needs to do, to save the day in the Final Hour. But that's the point that Ubisoft stops the story, cuts to credits, and starts working on the next game. So you end up with a narrative thread, based on a character that is given the amount of screen time, normally associated with a supporting character, or...a flashback family member. So they flip the structure on it's head, and the narrative suffers for it.
This is why I think the AC film actually is a lot better than people give it credit for, because they structure the different story elements properly. The focus of the film is on Cal, who is the one who can actually enact change, establish the stakes for him, establish how the Animus works, and why they are using it. They escalate the stakes as he gets closer to revealing the Apple, and they only delve into the past, for the length of a single action sequence, like a flashback should work. Cal is the one that has the character arc, has the moment of revelation of purpose, and takes actions that actually change events going forward. It's a well made film for the structure that the game franchise set up.