3rd solution - 3 systems. Perhaps a mini for the 3rd floor.

Why would you talk about a furnace in Seattle? Cheap hydro power and mild winters. Heatpump makes more sense. More eco friendly and cheaper to install and operate. Am I missing something?

People do NG because they are used to it and have experienced bad heat pumps. My crystal ball says costs of NG will have to rise because of AGW. In your area, electricity is pretty darn clean and would not be affected much by a carbon tax.

Having large systems zoned is difficult to get right. Of course it can be done but at no installed or running cost savings. I like the decreased maintenance and lower (perhaps) repair bills.

It is hard to have a system sized for a 2200 sqft floor also work for a 700 sqft floor.

I have hot water heat in S. BC where it can get damp in the winter , I love the heat it keeps every space at the same temp all the time with no hot and cold spots, it creates no dust and no noise. We added some Ac units at the ceiling for the main living space but our house is a 50s ranch with the huge overhangs that keep the summer sun out and allow it in in the winter . Most people where we are use heat pumps but I find them noisy but extremely effecient. IMO your issue is what are these spaces going to be used for? I like bedrooms to be cooler than my main living area and we have a walkout basement that is our media room and offices so I like that a bit warmer so we have 3 zones.

Some more things to add: there is no utility room on 2nd floor. So the 2nd furnace needed to be installed in attic (with access). In this case, is it preferred to have a smaller furnace installed in the attic?

I have zero experience with heat pumps but do have 34 years of experience with having two HVAC systems. My house is far smaller than yours - about 2800 sq ft on two levels plus an unfinished basement. The house was built in 1948. It's a 1 1 /2 story house that only had 1/2 the 2nd floor finished when we bought it, and they rarely used that bedroom at all.

We added a full dormer across the back of the 2nd floor, making two BR's and two ensuite baths. And we installed a separate HVAC system for this area. We like to sleep in a cool/cold room but don't want to freeze on the 1st floor. Right now, the outside temp is 39°. My upstairs furnace is turned to "off" as I see no reason to heat it with no one up there, and then to have to open a window to get it cold enough for sleeping when I go to bed tonight. it will be in the mid-50's when I go up at around midnight. I like it like that and am very cozy!

But this weekend, the temp is to drop into the teens so I will turn it on when I get up and have it set at 62°.

In the daytime, my 1st floor HVAC is set to 71° in the winter, and 73° in the summer (upstairs AC is set to 65° in summer and runs constantly).

It is cold in my basement - only one ceiling vent - so when I'm down here doing my breathing treatments or laundry and am on my computer (desktop is down here), I use a space heater.

Having two systems has worked very well for me. I have them checked/serviced twice yearly. I cannot imagine that a basement HVAC system could ever get my 2nd floor as cold as I prefer for sleeping. It gives me a lot of flexibility.

Having two systems is nice because if one goes out, the other will still work!

From past experience with different systems in different houses, I would go with 3 separate systems, like David Cary suggested.

Much cheaper to do it properly while building than trying to patch/retrofit/improve things in an existing house. We spent $38K trying to re-engineer our system, because my DH was really unhappy with the 2 systems in our house. I don't think it was worth the cost for the minimal improvements achieved. The new systems are much quieter at least, which is a positive!

Well, definitely don't try to get one system to work in your setting! I also don't trust new construction ("lowest bidder") HVAC installers to get zoning right. Honestly, a small heatpump for the attic is probably the best solution (or a minisplit if its not divvied up into multiple rooms). For the main two floors, I'd definitely use two systems. If you have natural gas, that's usually the cheaper solution from a fuel utilization standpoint but if you want AC also, then heat pumps would be less expensive to install.

You need to get someone to do an analysis of total cost over the life of the systems for heatpumps (electric) vs gas furnace/AC (initial install cost and fuel utilization for 15 years). Without this information, its very difficult to make an informed decision.

3x systems = 3 x maintenance

Two systems for sure, three for maximum potential on comfort. I have a single-story 2,570 sq ft house with one system. Largely an L-shaped layout with living area in the middle, master BR/BA at one end, 2 BRs/BA at the other end. Two returns, in the hallways outside the BRs at each end. The master BR and particularly the master BA at the far end, with west exposure and three large glass block windows, are consistently warmer in summer and cooler in winter than the rest of the house. I can't imagine trying to properly heat and cool three stories with one system when getting good airflow and consistent temperature across a single story can be a challenge with one system.

Our place is only 2300 sqft and we had HVAC contractors pushing for two units. I can't imagine doing one in 5k sqft!

Square footage can put a number of challenges in your path in trying to cool / heat a larger structure with a single HVAC system, especially when it comes to residential based systems.

The Seattle area is a more moderate climate so while it might be possible to achieve this depending on a large laundry list of various factors, it's still (for comfort sake) better if you put in equipment designed to handle each floor individually.

If you have the money for a 5000 sq ft structure, you should have the money needed to cool and heat it properly. If it's about cost and / or maintenance then build a smaller structure.

You can argue all day long about 3 HVAC units maintenance > than 1 or two HVAC units... but at the end of the day the argument is pointless when you consider the maintenance of a 5000 sq. ft. home versus a 2000 sq. ft. home.

If maintenance is of any concern, you're building too big of a house to begin with.

If you value comfort your best bet is 3 separate systems for each level. Due to the size of this structure maintenance will be a headache anyway... even if you skimp on the HVAC design aspects.

I don't know. I think maintenance is still important even if you can afford 5,000 sqft. Wealthy don't become wealthy by wasting money.....

I totally get the appeal of lower maintenance. Just not worth it here.

Maintenance costs are miniscule, compared to having to run the HVAC system constantly to make up for a bad or inadequate design.