Running barefoot is okay, just watch your arches. I have super-high arches and they feel like they're going to collapse when I tried it. As a result of the high arches, I also supinate rather dramatically and at the most inopportune times.
Since I suck at running and haven't found a shoe that I can wear for more than 15 minutes without parts of my feet going numb or getting sore, I tend to use the treadmill or trails and do inclines and declines at around 3.5 - 4 mph.
I broke my pelvis in '93 and my fibro flares terribly if I run too much, so I ended up doing :30/1:00 intervals of running at 0 incline, 6.2 mph and 8% incline at 3.7 mph on a treadmill and found the best cardio workout for me.
Doing this for stamina, I can make it for almost 45 minutes without killing myself.
That's a big step for me. As my ex put it... "there's a lot of movement going on back there" when I run. I'll get there, I hope.
I gotta get my "movement" back into the gym since the MRSA toe is almost healed!