I would get the ducts fixed. I would guess that he could be doing as much, or more with the returns than with the supply's. I think that you should be able to get away without the zone dampers system in a colonial of that size. When he does his new ducts ask him to make sure that every run has its own damper in the basement (manual not power). Start with all of them wide open. If he has done the ducts correctly you might just be happy and not have to do anything else. You are bound to have a serious improvement. Then, if you notice that the upstairs is a lot hotter than the downstairs you could close down the dampers for all the upstairs runs a little bit at a time to "balance" the system. Have whoever fixes your ducts put in wiring for one or two other thermostat locations, just in case you do go with zones in the future. I think these can be run through the duct work.
If he doesn't put a return duct into each room then you need to make sure that there is a 1.5" gap at the bottom of that room's door (when closed) and at least a large return duct in the hall or central area of each floor. Feeding supply air into a room doesn't do much good if the air in the room doesn't have anywhere to go, i.e. into the return. You won't get enough hot air out of it otherwise. You have a nice new system. Giving it the correct ducts should let it do its job, where it can't now. What you have now (your new furnace) is like a brand new car with wooden spoke canastoga wagon wheels - get some new tires (ducts).
The most important thing for you to do is to get quotes from at least three companies. Have them quote you without a zoned system and with a zoned system, unless they all tell you you don't need zones. Hopefully you have some well known, honest contractors in your area.
Electric heat is junk in my opinion. It is insanely expensive where I live and I have never liked the thermostats. Also you likely don't have enough capacity in your house's electric service and would have to improve your service and probably get a sub panel too.