If you can handle the pounding, I think training in flats is preferable as it strengthens your feet and ankles. I think there is something to the notion that having a raised heel keeps your feet from doing what they were meant to do. I am heavy for a runner and susceptible to pounding and I have to train in a well cushioned shoe to not break down during 100 mile weeks and I can really tell I suffer the consequences of weak feet and ankles - I am a pretty quick runner (certainly most of my peers race in spikes on the track) who cannot run in spikes because my feet, ankles, and calves aren't strong enough to run properly in them. In spikes I just feel like I am slapping and I mostly race in "performance trainers".
Maybe a solution to the "high heel" problem would be to add a little forefoot cushioning while subtracting from the rearfoot (like the Saucony Azura).