I have been making my cookies out of wheat flour lately and I haven't even been able to taste a difference.
These cookies were taken from an Oatmeal Raisin Recipe but I made a few adjustments.
60% Dark chocolate chips
and I replaced the White flour for Whole Wheat flour.
For some reason, to me, they tasted better after they cooled, it seemed like the dark chocolate was stronger tasting when they were warm.