I think the issue is people read “And they have a plan” and thought “And there’s going to be a twist.” Not just a reveal, a you-were-wrong-the-whole-time-about-a-fundamental-part-of-the-story twist.
The Cylons had plans, goals, plots, and schemes out the wazoo, I don’t think you can seriously argue that the show presented them as bumbling their way freestyle towards destroying 99.9% of humanity and replacing them in the cosmos.
Good God yes. I'm not sure why people/viewers get their cockles rattles by the whole "And they have a plan" thing. There wasn't. It was a tagline. End of line.
It's also not essential to the story at all.