What is 'best' is something that will vary from setup to setup. For those with larger flocks, and therefor larger enclosures to consider, a skirt is going to be more cost effective than a floor for the simple fact that it will take less wire overall to go around the perimeter in a 12-18 inch...
Rather than thinking of it as digging down a foot or more to put the wire in, think of it as laying a "skirt" around the pen - laying the wire out 12-18 inches. It doesn't have to be buried a foot down, or really at all (some folks put the wire skirt on the ground surface and cover it with...