And we need to be very clear about one thing. The Catalyst is not a billion year old super intelligence that has witnessed countless cycles and is making an informed decision. The Catalyst is a fictional narrative device that was created during the production of the third game by a very human, very not-a-billion-years-old member of the Bioware writing staff.
They can present the Catalyst as being infallible all they want, that doesn't make it so. And for the record, I don't think they do. The Catalyst has a major blind spot in that it doesn't just observe the cycles and thus make an educated decision. The catalyst actively shapes the cycles and thus influences the outcome. Indeed, the relays were built to guide technology in predictable ways to maximize the efficiency of the cycles, thus drastically reducing the chance of an unexpected outcome to occur. There is some serious bias in the Catalyst's thought process that the thing doesn't appear to be aware of at all.
And that isn't even the tip of the iceberg.
So yeah, thinking we can do better than such a flawed intelligence as that is not really arrogant. Age doesn't guarantee wisdom, especially when coupled with bad programming.