Tony, see
http://dspace.mit.edu/handle/1721.1/29737 to download a copy. Although I just checked it and it looks like a pretty rough scanned version. I guess I would read the first chapter and skim the rest to get a sense of the content and let me know if you want to read more and I will get you a good color copy of the thesis. You won't hurt my feelings if a quick skim is enough! :>) Although your note on systems complexity makes me think you might like it a little. My masters was in System Design and Management at MIT...Ford sent me just before the GT program.
Understood on the custom home and building for others. Clear system goals and requirements from the beginning help a lot, I believe- defining "what" is important before you start defining "how" to design it. Us engineers and designers (and people in general it seems) like designing solutions before we've clearly defined the problem, which hurts results in a large way, from my perspective. For sure your example with a new home owner coming in after the fact has some difficult challenges and sounds like changes to your original requirements.
For sure systems are getting more complicated. A clear vision (including requirements), Systems engineering and fundamental engineering (mechanical, electrical, etc) is required and the more predictive work the better. Many of us "racers" were put onto the GT team because of predictive capability. So yes, we used computer modeling signficantly for nearly everything. The auto industry has been using very capable 3D CAD since the 60's. The entire car was solid modeled in 3D in detail. And structural analysis, crash analysis, kinematic analysis, vehicle dynamic analysis models (My area predicting a cars dynamic behavior blasting around the track) aned more all let us get major things "right" the first time. However, good application of these tools takes signifcant hands on experience as well as having a good feel for the numbers, sanity checks and what results to apply when and what results to be skeptical. We would not have made any of our goals (performance, cost, timing) without significant predictive capability. For sure, you (the whole team) can't think of everything, but I believe you can get a long way there with the right people and the right approach. You will definitely note multiple areas in my thesis I would ideally do different on the car's architecture, but again within our bounds and some high level decisions made early in the program (above my pay grade) we came out with a very, very strong result.
I used a similar approach, 3D cad tools, systems engineering, energy modeling, etc on our very, very custom direct gain passive solar home design (including geothermal back up radiant heating and passive cooling). The design took a lot of time and included 12 fairly detailed design options before I finalized it. I can share more with you on it away from the GT forum if you would like and I would be interested in hearing more about your projects...residential build and it sounds like software and hardware integration.
Scott