A 2-stage furnace is quieter, can run more efficiently, and allows you to add a 2-stage AC. I personally like the fact that most of the time I don't hear my furnace and I don't get this blast of cold air down my neck every time it turns on. These are the common complaints of forced air systems. The 2-stage AC does a better job of humidity control which in my opinion is a great comfort feature.

Yes, it makes a difference to comfort as you don't have the furnace blasting on high unless it's really necessary. And, as Mike says, it dehumidifies better as it runs lower and longer in cool mode. Whether it's worth an extra $1200 is largely up to you. 2 stage furnaces are not inherently more efficient (from an AFUE stabdpoint) than single stage.