I've probably done this a hundred times, but here it goes again.
I had 7 stress fractures in high school/first year of collegiate running (~got a medical hardship, so did not compete beyond the first year). Wore several different types of orthotics and shoes and had numerous other overuse/nagging pains. I was basically a 19 min. 5K runner because I had never trained consistently for more than 4-5 months due to injuries (mind you, I'm a woman).
4 years ago this coming Dec. (wow, has it been that long?!) I was fed up with being hurt all the time and decided to toss out the orthotics, find a 'basic' shoe (~Asics Onitsuka Ultimate 81's), and work on building foot and leg strength. Did it cold turkey! I started from scratch on the mileage, and progressed it each month (10-20-30-40-50-60->70 mpw after 7 months). I ran painstakingly slooowwwww every day for about 7 months. I added barefoot running after about 3-4 months, and then at 7 months switched to the Puma H Streets. My feet/ankles were 'very sore' for the first 3 months (getting out of bed in the morning, owee!), but I had faith they would get strong and adjust (which they did, and the soreness went away). It was after 7 months of slow running that I started adding in things like strides, progression runs, short/long intervals, fartleks.
Going into that fall, I was a completely new beast, running in the 17's for 5K on the roads, running my first road 10K in 36:22, and my first 15K in 55:46 (all of which I have surpassed since then).
I have continued to stay healthy, progress my mileage each year (~now at 100+ mpw), and most importantly improve and run PRs. I train and race in the same shoes (~rotate between the Puma H Streets and Puma Cortlandt XC flats). I see it as an advantage to train and race in the same shoes because I've developed my body, in terms of muscular strength, proprioception, and economy, to what I race in. This was evident last spring in my first marathon, where I had very little muscular fatigue during and after the race.
To put it simply-- my body feels better in flats. It's a HUGE difference compared to how I felt on a daily basis 5-7 years ago in trainers. I wouldn't say it's solely 'the flats', because there's been lots of things I've done differently. I'm incredibly meticulous about nipping little aches and pains in the bud.... usually this involves a bit of barefoot running, wearing different or new shoes/socks/no socks, massage, or just a good night's rest. I haven't had a minor ache/pain I can't cure with barefoot running (including a whacked back from a bad mattress). I train on a variety of surfaces every day, but feel the most comfortable on roads/asphalt/concrete. I do my long runs (20+ miles) almost all on roads. I focus on lifting, rather than pushing, off the ground.
I don't believe this is for everyone.... it requires a tremendous amount of patience, experience, and committment. Simply understanding how the human body functions and adapts as a whole is important. For example, "Your Achilles is sore?".... take off your shoes and do a little barefoot running! "Your PF is sore?".... stop wearing those clodhoppers at work and get some flexible, low-heeled shoes! It's taking care of these little things that can make a huge difference. Too much, too soon... it's going to bite you! The human body is incredibly logical if we just listen to it and trouble-shoot a problem ASAP. You gotta think long term and let the body adapt and develop as needed.
Well anyways, I ran a 2:48+ marathon debut last spring and am looking to get the sub 2:47 Olympic Trials qualifier this fall. NEVER in my life did I imagine I would be healthy enough to train and run a marathon, let alone be good enough to have a shot at qualifying for the Trials! What a ride (and it's only just beginning ;))....