I seldom if ever get any flats whether it be my 700x23 road bike tires or 26x2.0/700x50 touring bike tires. The quality of rubber underneath you will make more of a difference in flat protection than the size of the tire (within reason).
2.0 tires are not overkill and they definitely open up more options as far as what kind of ground you can ride on. +1 for what oneredstart said about the Extremes. They roll amazingly well for a larger tire with tons of traction.
I agree with the premise of the BQ article in that maintaining contact with the road helps you roll faster not unlike a full susp mountain bike going over a rough trail. I just don't like the fact it's not explained how they came up with 15 percent being the magic number. There is so much missing in that short article on how they came to the conclusion. If I followed their chart, the only road bike tires I should use would be high pressure tubulars. No thanks.
If you are going with a 1.5 and 2.0, I would put the 1.5 on the rear and the 2.0 on the front to smooth out the road.