First, Your designer probably isn't a HVAC designer... If he's ever removed an air handler, or even a component, out of an attic, he'd probably be able to tell you there is much added expense incurred in dealing with the conditions of the attic (temperature & space) & keeping the house clean as he moves out the old & in the new. Up here in MN we have basements for our equipment.
Second, if he or anyone, is recommending flex duct, make sure they can justify the added duct dimensions required. Flex duct needs to be up sized at least one dimension in order to allow for the static pressure increase inherent to the duct. I've been designing HVAC systems for over 12 years now & never allow more than 6' for the final connection.
My recommendation would be a main floor closet installation (in the best of all possible worlds it would be a straight shot in from the driveway side door that would allow a 2 wheeler clear passage to & fro) The mains would be sized for a trunk serving the upstairs from floor diffusers & the main floor from the ceiling. I'd then try routing the majority of return air from high wall (or ceiling) mounted return grilles. The main floor would also have high returns. Remember the warm air from the main floor will migrate to the upper floor, so a return in the stairwell will serve as a lower level return. A SA & RA main would also need to be run to the 1/2 story attic.
Since I don't have load calcs I'll assume your running between 600-750 per ton. If the floors are 2000\\2000\\1000 sq.ft. your looking for between 2-1/2\\2-1/2\\2 tons to 3\\3\\2 tons. (Have your local contractor verify these loads before signing anything.) In this case I'd install a unit on the main floor with ceiling SA & RA grilles & a 2nd unit on the 2nd floor serving floor & ceiling grilles as noted before. (of course the 2nd floor parking level would allow a straight shot as well LOL)
If most of the areas are on the main floor, I don't see a need for zoning, but a simple system should be easy enough to install for the kitchen & other spaces. Zoning the upper floor might be required for master bedroom suites, bedrooms, office areas, etc... but without plans I wouldn't venture a guess. My background has leads me to believe a well designed residential system, with proper installation (i.e. no flex) & a decent air balance, with a room by room heat loss & balance report, won't need zoning.
In an effort to produce the maximum amount of flames, I'll go further & suggest these options: If I were to zone 2 systems on 2 levels, as afore mentioned, I would install bypass dampers that dumped the air to the other level via grilles serving the space rather than directly back to the return of the zoned system.
I would consider installing an air source a heatpump to one of the 2 systems, probably the lower & use electric strip for heat in the other, that would all depend on electric & gas rates, & cost of up grade. Truth told I'd install HPs on both systems. High Seer cooling & staged heating...
I will never consider a constant volume blower in any home I'd build. I replaced a CV with a variable speed furnace a couple years ago & have been saving $15.00 a month on electric with the fan on constantly, which by the way is the best way to insure even temperatures throughout the home. On that I'll stake a claim.
Just remember, why would you want to cut corners on your future comfort... Why save $5000.00 to be uncomfortable in your $500000.00 home (prices may vary) Pay for decent equipment now by forgoing the granite counter top etc... In a few years you can "remodel" the kitchen by swapping Formica with granite, upgrading the faucets, etc... then the wife will be happy a 2nd time.
Now I'll don the firesuit & read the replies...
good luck geothermaljones st.paul,mn.