think system. a unit is just a component in a system of components. correct and effective heat transfer depends on a lot of factors including well designed duct system. regardless of the brand you buy, if you go with upper end technology, make sure someone is matching these components properly and the ducts are adequately upgraded as well if they need it.
believe it or not, it is possible that a higher seer, 2 stage system with a variable speed blower and humidity sensing could suit your needs if designed properly and your house is well sealed and insulated. architecture, windows, insulation and a host of other issues should be evaluated. a manual j may be necessary.
the obvious advantage of 2 systems besides better addressing your specific heat load areas, is the fact that if one goes down, you are not dead in the water. you have to weigh out the cost vs the advantages. zoning works in some applications. in the wrong application, it can be a nightmare. try to gain some understanding of exactly how it will work in your situation before you commit to the idea. this will require someone to consult with you and lay out some suggestions. ask a lot of questions. ultimately, if you use the wrong contractor, you will be paying for that mistake for a long time. good luck.
by the way, i would avoid the guy with a $1200 fan motor.