Numerous contributory factors for me:
1. My riding is tending more towards big mountains and tech descents, so flats suit me for both the hike-a-bike climbs and the tech descents. Good all-round compromise.
2. Getting clipped into spds was sometimes an issue when there was no easy run-in to an obstacle.
3. More feedback and less float. First thing that I noticed on first day on flats was that there was slight wear in the swingarm bearing. Never felt it on SPDs.
4. Consistancy. I have a few bikes, ranging from 180 F/S to 140 H/T. Flats work for all of them.
5. Wear. SPD pedals and cleats both wore out pretty quickly for me, and with a few bikes/shoes wearing at different rates, interchangability between which pairs of SPD shoes on which bikes was just overcomplicating things.