I have always figured that scanning a negative is a better option. If you scaned a 4 x 6 at 600dpi, you'd end up at 2400 x 3600 pixels.
A 35mm negative (24x36mm) equates out to a 0.945 x 1.417 inch negative, scanned at 4000dpi would get you a pixel count of 3780 x 5668.
I also think you using a negative scanner gives you a higher color depth. Maybe part of the scan being better is that the negative is scanned against a light source behind it, where a print is a reflective image
