Most people don't have a paint booth with adequate exhaust to control overspray or fumes, so I think painting in pieces is better as long as you can get the color matched. Another thing that helps is to make sure you have all the pieces hung the same way- hang the left and right fenders the same orientatation, same as the doors, etc, so you spray at the same angle for everything. In pearl and metallic paints the gun angle really affects how the color looks.
Also, most people don't really have a big enough compressor to paint a whole car without causing big variances in pressure or moisture as you go around the car. Painting one panel at a time helps make sure that you don't gain moisture in the air as you go along and that you keep the same pressure all the way. I like to use a regulator right at the gun and record the pressure setting to make sure I get it the same every time I paint with that paint.
