The most active HVAC forum is at http://www.todayshomeowner.com/forums/heatingcooling.html. Your question has been asked many times there.
Get a manual J evaluation for heat loss and not a rule of thumb per sq.ft. Some utilities offer rebates for high eff. furnaces so check that out to see if it is worth it or not.
Besides the quality of the units which may be comparing apples and oranges, check the contractors references for installation issues and call back issues. Look at warranties and services charges for call backs.
I don't know about size/consistancy and thin air issues. Are you adding a/c also?