American Cheese really isn't all that bad for you - it's just been emulsified with extra water to make it melt better and not separate. The resulting processing however makes it taste more bland. But in many cases, the overall ingredients are still rather similar to regular cheese - unless you are getting some really cheap brand, or a lower fat variety with fillers. I've heard throwing a slice or two of it into a cheese sauce will help keep the other cheeses from separating too.
My favorite grilled cheese is with smoked provolone and sharp cheddar, on some crusty Italian bread with either butter or mayo on the exterior. Believe it or not, mayo works great on the outside of the sandwich when frying it. It gives it a great tangy flavor and a nice golden color. Some people are often worried it will be too greasy, but if you think about it, butter has a higher fat ratio than mayo.