The size of the pan makes a difference. I remember going from what was probably 9x9" to 8x12, and found it tasted different. The bigger pan made thinner brownies and they were more thoroughly cooked, drier and less chewy. I preferred the thick chewy brownies cooked in the smaller pan.
9x9 is 81 square inches and 8x12 is 96 -- and that made a big difference in taste. (I'm not sure about the pan sizes, though; there might have been more difference than that.) You might be able to compensate for the bigger pan by adjusting cooking time, but I suspect you'll never be able to make thinner brownies taste the same as thicker ones.
Pans are cheap; why don't you try different sizes.