I have ducted in my home (installed by previous owners). But I'd go splits if I had a choice.
Not sure how modern zoned setups are rigged, but with ours we have outlets in every room, but only the one filtered inlet in the hall. So that means you must leave an air path from the rooms you have selected to cool, back to the inlet, or else you'll starve the fan. This means you'll shorten the fan life, get no cooling, and waste power.
For example, lets say the inlet is in the centre of a home, surrounded by kitchen (zone 1), surrounded by living rooms (zone 2) surrounded by bedrooms (zone 3). In my case I can turn on only zone 3, but need to allow airflow back through zones 2 and 1, so I'm partially cooling them as well.
With a split system you can cool just the one bedroom (or one zone if you have more than one unit hooked to the outside pump) as the air stays in that room recirculated through the wall unti. If the pump is running you may as well turn on all the connected interior units.