Couple questions before I recommend , Is the total tonnage the same , Is one company more experienced/professional . On the three zone system would a static bypass be used or a real dump zone ( a static relief damper tied to a vent into the living space ) . Are the warrant tees/ efficiencies comparable . there may be many differences in the systems then the number of them and the price most important is the company that will be in your house , and a responsible and ethical company would be happy to explain why they designed the system or systems the way the did , ultimately your the boss but there may be a perfectly logical reason why two systems is recommended ( like the ability to get sufficient duct work to the second floor , or airflow concerns with a three zone system , as you restrict airflow or increase its temp like with a standard dump bypass your eff goes down)
Just my opinion