There are a lot of issues here and a properly done zoned system is not necessarily cheaper - there are a lot of variables.

If you use a better staged system (which you would really have to do to make it acceptable), the efficiency would probably be higher. Think of it this way, $4000 per unit or $7000 for an efficient, staged larger unit.

Maintenance is 50%. Advantage single unit.

If you have NG, and the single unit is in the basement, it will likely be a 90%. If the second unit is in the attic, it will likely be a 80%. Advantage single unit.

Conventional practice in the SE is 1 unit in basement/crawl and upstairs unit in attic. If you do a single unit, it would be in the basement. Advantage single unit (since the attic has far greater temp swings). The advantage here is on efficiency and life of the unit. Even the refrigerant runs are shorter to the basement - more efficient.

Single unit outside - better use of outdoor space. Advantage single unit.

I definitely don't think the answer is always 2 units are better than one. If you can be in the spec homes and try out their zoned system and it is acceptable to you (or unnoticeable), then why not? But you really want to find days that need HVAC a lot and there aren't that many in our future. But you could go and play with the stats and force it to run hard. You definitely should have stats on both floors.

I have a two floor house with two furances and condensers. Both furnaces are in the basement and share a common return duct. The air flow to the upstairs bedrooms is good and temperature is even.

My HVAC contractor gives a break on annual maintenance for customers who have mulitple systems. I don't pay twice the amount for the service.

atlnon, How many zones does this single unit house have , is it a split system High SEER system or a basic ducted unit ? If it is a split system with or without ducts it is a very efficient system that will save you money right from the atart of your residing in the home . Ducted or non ducted splits are far superior to the system you are familiar with . Being able to camp out in another part of the house is a plus during a breakdown but these are quality units that work much less hard and are very dependable besides you saving a load of money on a monthly basis .

The single unit has 2 zones (first floor and second floor). I do not know if it's a split system High SEER system or a basic ducted unit. I will find out. However, I'm trying to understand what you mean by a split system (vs. basic ducted system). Aren't all traditional (basic ducted) central HVAC system a split system where the condensing unit is placed outside the house, and the evaporator coil is inside?

HE is referring to a mini-split which vary few in the US use and certainly not in a spec house new construction. These are more efficient but would be significantly more expensive to install in a large new construction setting.

"split" here means "mini-split"

To Mike - I've seen both - 2x for 2 units or less but it wasn't that much less than 2x. Your dual units in basement is not done often in the South. Sure it is preferable but does require a significant chase and significant extra cost. That cost is balanced in the OPs case by just getting 1 unit.

OP - you really need to find out if the system is staged. What you don't want is 5 tons firing upstairs only on a cool night when you just need dehumidification. This is where the single system really fails. Now if you are comparing 2 units that are single stage to 1 unit that is 2 stage, there is little difference. Mostly 2 units still has the advantage here but if the system is a Carrier that 1st stage is 50% and your floors are roughly equal in load, it is no different. If no different in this worst case, then the advantages really shine.

Of course, given the option, most people who really care would want 2 units both with 2 stages in your climate (that is what I have in NC).