It's a pretty good article.
In that era I saw two major misconceptions around minimalism in running footwear. The first is the idea that heel-to-toe "drop" is the the main important metric -- of course, a shoe company thing. Actually what matters a lot more is proprioception -- the feeling of knowing where your foot is in space relative to the ground, and also the feedback your foot is getting from the ground.
The second misconception is that it's important to switch over 100%. Related to this is a misconception that somewhat more minimalist is better. As a competitive runner, I saw benefits from mixing in barefoot strides and a couple miles per week barefoot on soccer fields while keeping my training shoes the same. I'd recommend others do the same, and very gradually increase mileage.
The challenge for research in my understanding is that it's very hard to track long-term injury prevention and performance improvement in a statistically significant way. You can measure what happens when habitually shod people do a barefoot run, and you can go to Kenya and study how habitually barefoot people land when they put on shoes, but that's different from the long term impact on your gait of changing your footwear for a long period of time. (I'm not a researcher myself but I've talked to them.)
I think your proprioception point is huge. I sometimes randomly get a floppy foot. In anything but structurally sound shoes, I'm wrecked. Would barefoot running have avoided the problem or exacerbated the problem?
No idea, honestly. Normally I'd think a few minutes at a time of barefoot jogging on a soft surface isn't likely to hurt and might help.
You are highly highly aware of your feet when running in shoes with 3mm of total rubber/padding.
Same experience here (though I probably skewed more to barefoot than you did). There's a certain amount of immediate painful feedback for a heel striker once you start running barefoot. There's a certain amount of reconditioning and retraining of under utilised muscles that needs to happen so I think your advice to gradually introduce is make a lot of sense. What I've always found interesting is that even for runners like me that had poor form, as soon as the shoes come off we naturally shift towards a more efficient and lower impact technique.
After a few years of regular barefoot running my running gait had changed enough that I didn't feel the need to keep doing it and have been doing runs in race shoes almost exclusively for the past decade.
It's funny that people will hear about something new, misinterpret it, and then get angry about it.
what brands get proprioception well?
I think anything whose soles are really thin and not too hard. I'm partial to Xero, but there's a lot of possibilities.
I do think all shoes, except those original Vibram Five Fingers, are not a great substitute for barefoot running itself. Running barefoot on a nice grass field feels so much nicer and more fun, too! But the minimal shoes do help force you to feel the ground and not just slam into it, so I think they can help.
Whatever you do, I'd only make changes slowly: try 10 minutes of barefoot running or with different shoes, a couple times a week at the end of a normal run, and go from there.