"Ark Contingency" is a pretty damn fatalistic name for an initiative. But I guess that fits since the only reason the ark-theory version of the trip to Andromeda would happen is out of fearful assumption that the Reaper extermination succeeded, something that's going to follow the story around for its duration. Hell of a way to move on and move forward.
Yeah. Although it's stretching that no one mentioned this to Shepard, I'm starting to come around to the idea that this was a secret Council project. As I said the Citadel DLC established that the Council always believed Shepard that Sovereign was a Reaper, and continued to even though they told Shepard otherwise. The counter was always "then why didn't they freaking do anything?" Well, assuming they didn't want to incite panic, keeping an Ark Contingency secret from the public makes some amount of sense, and not telling Shepard about it in ME2 at least makes some amount of sense given his Cerberus connections.
Let's also be real here: if this was the Council's plan, it makes a hell of a lot more sense than what Shepard was doing in ME3. If the Council takes the claim of billions of years of harvests seriously, then the only conclusion should be to find a way to run instead of fight.
Does all this take some headcanon and sketchy logic about why none of this is brought up during ME3? Sure. But you could also have the Council say that Shepard wouldn't listen anyway and was too stubborn and deadset on fighting, which is actually pretty consistent with virtually every way you can RP Shepard in ME3. I'd be amused at such a dig from BioWare at their own writing, as well.
"He told us his plan was that we fight or we die! I mean, what an idiot!"