Which Saren and Benezia say they believe. And visions. And the beacon, which was a thing Saren took incredible risks to get his hand on. A risk which blew up in his face, as it happens.
Saren and Benezia aren't independent sources, so that's basically one person's testimony.
And it's an extraordinary claim. Think about it from inside the setting. These characters don't expect scary monsters from intergalactic space, so they're going to need extraordinary evidence before they believe it. The council doesn't believe the story. Why must Shepard?
So, Shepard believes that Saren and Benezia are lying and the Council is right, but is arguing with the Council because reasons, and then will fly off to do nothing about Saren, and then God saves the galaxy from Shepard's incompetence by delaying Saren just enough for Shepard to stumble into the truth?
What? No. Saren's plan just takes longer. Why? Why wouldn't it? Within the playthrough, we don't have any reason to expect the plan to take a specific amount of time. For you to know that Saren's plan is waiting for you, you need to metagame.
As for why Shepard argues with the council, I frankly have no idea. I had no control over what Shepard said in those games, so I mostly ignored it. There was no other way for me to extract any enjoyment from playing them. Shepard's remarks only matter to me when I get to chose them, and I got to choose them zero times.
If you want to say that Shepard should have been allowed to disagree with Anderson and everybody else and side with the council as a matter of RP, I can see it, but that didn't happen.
That he doesn't say it doesn't mean he doesn't believe it. I don't understand why you feel the need to hold Shepard's remarks to be 100% honest 100% of the time.
And that still doesn't explain why Shepard and the Council should be preserved from their own stupidity.
There's no need for that.
It's not our job to keep the game world credible. It's the designers'. If I have to worry about preserving the integrity of the game-world, I'm not playing my character anymore.
The problem is that you're manufacturing incoherence by metagaming.
If you act in a way that maws sense for your character, and then view the game world's reaction to those actions from an in-character perspective, you're not going to see a lot of incoherence.
I want to be able to make mistakes, and be punished when I do make them.
Why do you need the game world to be identical across multiple playthroughs?
When I replay a game, I
replay it. That means I discover all the parts again from an in-character perspective. If something in one playthrough is incompatible with something in a different playthrough, who cares?