Actually what I was saying is that once an installation moves beyond cookie cutter then costs skyrocket. The problem is that anything that isn't absolutely plug and play will almost certainly require a lot of extra attention and because that work is only amortized over a single system it gets very expensive.
Its not that anything is "wrong" its just the nature of doing a one off job. Ideally what happens is that new and better technology becomes mainstream and standardized so that its cookie cutter driving down the installation cost and making it competitive.
We are beginning to see that with one of my favorite products a high efficiency furnace with heat pump. Its a complete system including the controller that automatically choosing between heating with gas or using the heat pump based on the outside temperature. That seems like a very good idea and it shouldn't add but a small amount to the equipment cost and nothing to the installation.