I had the same problem in my house and eventually tweeked my dampers in the basement to the point I got the upstairs to be pretty close to the main level temp. When we bought the place in the warmer days the upstairs could be at least 5 degrees warmer and in the colder days it could be about 3-4 degrees cooler. I figured out which branches fed which parts of my house coming off the HVAC system and shut the damper about 50% that fed the main level of the house and closed up a few vents on the main floor where the temps were fine with only 1 vent open in that room or area. In the summer I always close the vents in my basement.
It's just a matter of trying to route more air to certain areas of your house through some trial and error. The further it has to travel it will not heat or cool off your upstairs as well but there is no reason to freeze out or burn up on the main floor in order to regulate your upstairs more. Just shutting some vents and partially closing a damper to that floor of the house from the basement will force more air upstairs. Heck last summer when I finally got things adjusted it almost got colder upstairs than the main level on the really hot days when the AC ran more and noticed this past winter the temps on both floors were very close. I put digital thermometers that also have the humidity levels on them on all 3 levels of my house and especially during the winter it helps me adjust the humidity level on the whole house humidifier.