The first consideration is: what size does he really need? He can do a free heat estimate at http://www.hydronic.net Then he can consider what the new unit will do for him. A 100,000 btuh unit in a house built 20 years ago would usually handle a 2500 square foot house. As most houses built that long ago were about 1200 square feet, that is an oversized furnace, unless it really is a 2500 square foot house with R15 walls and R22 ceiling.
Many contractors throw in 2-stage furnaces without doing a written heat estimate, (which actually is required by many munisipalites now), knowing that the second lower-input stage would take care of an installation that required less heat. They then feel safer that 1/3 more heat is always available if the guy adds on to the house later. Nice idea, but it is not the purpose of a 2-stage furnace to run forever on low fire. Some people might consider a stake-body truck to pick up groceries for the holidays.
A 2-stage furnace is meant to extend the blower-running time so comfort is maintained, instead of having an oversized furnace run for 10 minutes and shut off completely while tha walls cool down for another 15 minutes. Today's ignitions are finicky and consider the result of making a furnace double its start and stop cycles by oversizing, almost guaranteed more frequent replacement of fan motors and ignition parts. A 2-stage unit often goes on high-fire to quickly warm vents and then goes to low fire after a few minutes. An oversized unit will make noticeable changes as it goes through this procedure.
So go through the 'normal' procedure of performing a heat estimate as suggested by manufacturers and often required by municipalities and utilities. I know it takes an extra ten minutes estimating room sizes and putting numbers in boxes on the computer; precious minutes that are taken away from the football scores. But an oversized unit is something to live with and regret for a decade until 'fed up' and redoing the job right.