Here's my opinion, take it for what you will.
Zones systems are really nice when they are designed for a certain application (ie huge houses, office areas ect). Using a zone as a bandaid to fix and airflow problem might work, but it's still a bandaid.
2 units are great in a 2 story house... but it costs more. Also with this being an old home (not in the process of building), I'd avoid this simply for the fact you'd have one unit thats really over sized and the added expense.
To me it really sounds like the ducting needs to be re-worked or balanced. Unfortunately this isn't the easiest thing to do, so it will take a contractor with some good experience designing/trouble shooting duct systems. If the duct is easy to access, and there's enough room to make size changes as needed, or install dampers in other areas of the duct to push the flow to where it's needed, then this is the best answer (again, in my opinion). On the really extreme days, both hot and cold, you may have to run the fan all the time to help keep the air circulating, but thats not a big problem.
Are there any return runs in the problem areas? If not, this could also help fix the problem aswell.