Improperly sized ductwork would cause uneven room temperatures. If a certain room is always not getting enough heat/cool then you could have a ductwork issue. Return or supply could be undersized or oversized.
I do believe that the ductwork is sized properly. I also think that zoning won't be a good idea because there's only three bedrooms upstairs and I wouldn't be able to afford it.
Be careful on the sunny room. It will usually be warmer than the rest unless zoning is implemented. Cutting airflow in winter to cool the room off would make it hotter in summer. Our master bedroom we like it cooler year round. A simple manual damper in the attic is what I used. Open fully by summer, open about 1/2 way in winter. "redneck zone control" if you will :)
Location of the return helps, but it's normally determined when the house it built. Low returns help in rooms that are cold all the time, high returns help in rooms that are hot all the time. I considered installing a high return to our master bedroom, but the damper valve was easier to install.
All of the returns are located in the ceiling since the furnace is installed in the attic. Our basement system is different with the supplies in the ceiling and the returns on the lower wall.
The redneck zone control won't be as precise, will require some manual fine tuning on your part, and will require a trip to the attic to change it once a season. If you can live with those shortfalls, do it the easy way :) A 2 zone control will be more complicated but offer more control.
Update.... I talked to the tech yesterday when he was here about zoning and the price was too high. I'm starting to think that since my daughter is off to college next year, my son could just move his bedroom to her room or to the basement. Pretty much that means that we will say no to zoning or adding a manual damper and have my son go ahead and move to the basement if he wants to! Or he can just dress in more layers while in his current room! ;) Thanks for all of the advice anyways.