Guest's comment brought up another thought - if you get an architect's mechanical designer or an HVAC company that actually "designs" rather than just "sizing" your HVAC system, there are a number of things you can do to get better air distribution and balance through the house. These include:
1) using multiple zones off a central air system - commonly the most efficient and "normal" - starting with simply running different branch runs of the main air handler duct to the different "conditioning environments" - which can be different branches to different floors, or in south-facing houses with lots of windows sometimes to north versus south facing rooms. Simplest approach starts with manual regulation of airflow using manual dampers at the branch split or by regulating airflow room by room with adjustable registers.
2) This can be made advanced by using different thermostats on each floor and then electrically controlled dampers in the ducting to regulate how much air goes to each branch - which can be further refined within a branch by manually setting register openings. Not a major cost to go to that step.
3) This can be bumped up a level by individually regulating registers with individual thermostats - there are electrically controlled adjustable registers now.
4) Or enchancing coverage in one area which has signficiantly different conditions with secondary thermostats or humidistats controlling a recirculation fan to increase airflow through a specific high-humidity or high-temp area. This is particularly useful in high-humidity areas like basements where you can tap off the feed duct to provide air to the basement to increase airflow and remove humidity, taking the airflow right back to the main duct with the more humid air at almost the tap point using a scavenger fan, so that higher humidity is injected into the air feeding the rest of the house. In high-temperature area the same thing can be done with the return ducts, recirculating some of the return duct air through the basement to dissipate some of the airflow heat in the return duct to the cooler basement before returning it for cooling by the A/C. Of course, such a method can sometimes need a humidistat in the system to keep from causing such high humidity that you get into mildew/mold growth conditions.
5) This recirculation method can also be used independent of the central air system in areas that are adjacent to but not part of the "conditioned space" to reduce the temperature imbalance across walls which can add heating or air conditioning load. For instance, it can be highly energy efficient in certain situations to pull roof-warmed attic air through a filter and independent fan to circulate it through the basement, both to remove humidity and to heat the basement, then vent that high humidity air outside - basically getting the heating of the basement for free down to as low as about 40 degree outside air temp in areas with good solar heating of the roof and attic.
6) One critical thing for new construction or modification jobs is getting the ducts properly installed - low-friction bends, proper sizing and distribution splitting per the ACCA manuals (so using an ACCA member company is a good idea to get a generally higher standard of design), using rigid rather than flexible ducting, insulating the ducting where appropriate (generally all ducting running in or outside walls/ceilings/floors that form the boundary of the conditioned area), making sure (and this is a very common area where workmanship is sloppy) using seam sealer in the joints as they are assembled to prevent unintentional losses or short-circuiting of conditioned air, and DEFINITELY NOT allowing 'panned joist" ducting, where the floor or attic joist space is used as an air passage in the HVAC system without ducting. This is just a waste of energy because of the significant losses of conditioned air to places you do not want it to go - not to mention the extra dust you pick up from overlying floors that are carpeted and dribble dust into the airflow.
Certainly in your case a single zone for that size house, especially if spread out or multi-story, would be a major design flaw - and if a builder proposed that I would demand a more expert designer do the design of the system. Proper design will get you a LOT more for your $ than a higher efficiency system will.
One thing not previously mentioned - is your house being built to a specific energy standard ? Going to a reasonable level of insulation and air tightness (without going overboard) will also get you a much higher return on your money than a less efficient house with a more efficient HVAC system - plus using a post-construction but pre-closing energy efficiency rating test actually PROVES that you got an efficient system, whereas with an HVAC system unless you get specific performance testing done on the completed system you have no way of knowing if you actually got the efficiency that you paid for.
