1. I was coming back from an injury, so I was running low mileage anyways. I completely chucked my orthotics and trainers right from the start of my comeback 8 months ago and trained exclusively in the Onitsuka Ultimate 81's. For someone that's in the middle of high mileage, you could probably simply cut your mileage/intensity down some to let your legs/feet adjust. Add in a little bit of barefoot running as well; this seems to ease the adjustment and make your legs/feet feel really good. As someone else mentioned, wear shoes with lower heels that are more flexible. I have some rope sandals that were always awkward to wear before I started training in flats-- now, with stronger legs and feet my rope sandals are the most comfortable shoes I own! I've also transitioned down to the Puma H Streets, which seem to be as minimal as it gets. I had never been able to get over 62 miles a week healthy in trainers with orthotics, but I've felt great running 70+ miles a week since June.
2. I think I already mentioned this.... there's just soreness, mostly the ankles. There's simply more movement in your ankles; more stretching of the tendons in your feet. But the stretching is normal; tendons are meant to stretch, not be restricted and tightened. I was actually more sore when I was getting used to the Ultimate 81's verses the Puma's (which are more minimal). Also, it feels kind of awkward at first in flats-- you body adjusts so that you land the most efficiently. My stride has smoothened out soooo much in the Puma's (since when I first ran in them and could hear my feet slapping concrete). Instead of landing exclusively on your heels, you learn to land more flat footed, which is how you land barefoot. I haven't had any knee OR hip pain since switching to flats; your feet can better sense where you step and make adjustments accordingly. Your tendons stretch to a greater degree and absorb the energy and disperse the force before it's transferred up the legs. My legs recover quicker after harder workouts.
3. I am young (22), but I have an injury history to boot (including 7 stress fractures)! I just don't see how trainers with orthotics could be any better towards your lower body than flats. My whole lower body has gotten so much more "relief" in flats than I could have ever imagined in trainers! I've been able to train more consistently with less problems. However, if you've found a shoe and/or orthotic combination that works for you, stick with it. I never had much luck with that route, so I was willing to try something radical and it's worked.
4. I have flat feet and overpronate. They say that flat feet are weak feet (hence, they can't control the excess motion adequately). Instead of keeping my feet weak with trainers and orthotics, I've strengthened them with flats so I don't suffer the injuries associated with flat feet. Honestly, I don't see what's so bad about overpronation and why there's such a need to control it with shoes/orthotics. In my case, I found that orthotics simply transferred the stress from my feet to my knees and other joints and bones. Also, your feet are meant to pronate to an extent, and there's MORE pronation in shoes than when running barefoot. Thus, flats help you to get as close to running barefoot as possible and decrease the degree of overpronation; you're simple more stable on your feet.
Just think of how much less weight you'd have on your feet if you wore just flats for a marathon! Less energy needed to pick up your feet up step after step after step.... To think that having MORE under your feet will decrease the force on your legs is FALSE. The following links are invaluable resources....
http://www.sportsci.org/jour/0103/mw.htm
:
http://www.coolrunning.com.au/general/1997e003.shtml
http://ww2.mcgill.ca/uro/Rep/r3111/robbins.html
http://www.triathletes-uk.org/info/running.html
http://www.pponline.co.uk/encyc/0636.htm
http://nhscc.home.comcast.net/l3_paper.htm
http://www.barefooters.org/key-works/case_for/3.health.html
http://www.geocities.com/jsgilbody/Gordon_book_040104.pdf