Installing A/C ducts, then A/C unit at another time ...
Could use a bit more info, is there a second floor, how old is your current equipment, do you have the required electric for the new equipment, are you planning on staying in the house for a long time, etc, but I'll give it a try.
By adding a new kitchen your going to increase your electrical requirements, I don't know if you have sufficient service now, are upgrading with the kitchen addition, or have enough for the kitchen but might need an upgrade if you install central air. But that should be one of your first considerations, make sure your electric service will handle the additional loads imposed on it. A central AC unit and air handler use quite a bit of electricity.
If you have the necessary electric you then need to size the AC unit correctly, if it's to large it will turn on and cool down the area to quickly, the AC needs to run for a while to remove humidity, if it's to small it won't cool well. So you should know what areas your going to cool, just the kitchen or the basement and first floor, this will make a difference in the electrical requirements. If you end up only cooling the kitchen it would be cheaper, easier and more efficient to use a through the wall or window unit. A central AC unit for a 20'x13' room would be very impractical. Another consideration would be that adding central AC to only the kitchen will not increase the value of your home, but adding central AC to the basement and first floor will.
I am going to assume that since you said your basement is finished that they are going to have to tear it up a little to add ducts for the new kitchen. This would probably be a good time to do all the work rather than having a mess now and another mess when they add the additional ducts. It would most likely be cheaper to have all the work done at the same time when the walls are open, and it's not fun living in a house under construction. While there's not much to go wrong with duct work, you might find that when you install the AC unit later that there's a leak (annoying whistle) or problem that can be addressed if everything is installed together an tested.
If your current heating equipment is old you may even consider adding a furnace, it's not much additional work if your adding central AC and ducts for it (assuming there's no second or third floor). A newer furnace would be a lot more efficient and you wouldn't have to put baseboard heat in the new kitchen.
I may have complicated the question. If putting in a couple ducts for the kitchen is cheap, I would do it, but if they have to do some demo work in the basement and it's going to be expensive and/or you don't have the necessary electric or are not going to cool more than just the kitchen I wouldn't bother wasting the money.