There are three separate issues that I identified need solving.
1. Adequate ankle support.
2. A shoe that reduces supination
3. Foot discomfort.
1. If worried about ankle injury and want support, the shoe or boot is not the answer. You really do need an ankle brace that is designed to wear inside shoes. A shoe or an mid-height (just above ankle) work best with such a brace. Boots with high tops can provide some support, but they will not act as effective splints to keep injuries from occurring. See additional comment below.
2. For supination/pronation, look for a shoe that is focused on motion control. Most manufacturers will have them. These models will have a 'straight last' rather than the typical 'foot shape'. Hold the shoes upside down that have a straight last and it can be hard telling the right from the left shoe. Filling in the 'cut out' of the narrow part of the 'foot', tremendously reduces supination or pronation.
The shoes will also tend to be 'stiffer' with increased stability (different than motion control), a wider heel and a reinforced heel counter. The midsole will contain materials that are firmer to help counter breakdowns at the outer edges of the shoe. There will also be more support structures build into the shoe to resist breakdown caused by pronation or supination. Also look for shoes rated for heavy individuals.
3. Discomfort in the heel may be due to a mild plantars fasciitis which certain exercises can help control. In the forefoot, a bruising pain is commonly caused by prominent metatarsals, and metatarsal pads that are properly placed on the insole will help provide relief. In a motion control shoe, there are insoles that are very cushiony and can add to whatever cushioning the shoes midsole provides.
Brooks and New Balance are two manufacturers long known to make motion control shoes, but certainly not the only ones in today's marketplace.
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Individually held preferences are something which cannot and should not be debated. Folks have a right to make choices based on whatever criteria they believe is important to them. To that end, I want to say that whatever your reason for wanting boots, flip-flops, bare feet, sandals, trail runners, etc. do not feel that you must change your decisions based on what 'everyone else' does. Be comfortable with your choice.
That being said, I think that it is important to look more closely at this issue to provide helpful information for those, who are trying to make informed choices, to consider.
It is not my intention to offend anyone, as I believe that there are times and situations where boots are a reasonable choice to make when hiking, backpacking, or walking. I own and use a pair of Lowa Camino boots in certain seasons and weather conditions in the mountains when backpacking.
However, there a lot of people on this forum looking for answers about footwear and want to make decisions based on what is factual criteria. If you are looking at boots as a footwear choice, ankle protection is not a reason to do so. While boots can provide additional support to the ankle, their effectiveness appears to be no more significant than trail shoes or trail runners when it comes to preventing injuries.
There is a long held belief many share that boots provide ankle protection from injury, not just support. Yet, long term studies and research have shown this is not quite the case. Above ankle boots may provide additional support for ankle structures when carrying loads, for example. However, the issue of protecting an ankle from injuries, as some may argue by citing other studies, prove this IS the case. However, when such studies are carefully examined in order to break out the types of movements engaged in, levels of exerted force with sudden direction changes - like basketball - , weight bearing and loading of lower leg structures, and the type of activity engaged in when injury occurred, such studies have n direct correlation to backpacking or trekking as an activity.
It appears clear that unless there are existing and specific diagnosed medical issues, for the vast majority of individuals the ankle is best protected with exercise and use, where the ankle is required to react to uneven surfaces, exercise, and balancing on one foot in order to build strength and endurance and lessen susceptibility to injurious fatigue.
The only sure and viable ankle support for protection for those with a medically indicated need, are ankle braces which can fit inside of the shoe or boot. Despite anecdotal evidence and subjective opinion to the contrary, research has repeatedly shown that boots by themselves do not provide the level of stiffness and the shear rigidity needed to keep ankles free from injury.
They can, in fact, exacerbate the risk of injury.
A foot snugged up inside a boot is sitting higher off the ground than when in a shoe because a boots' outer and mid-soles are much thicker and built up. Additionally, the outer sole of boots are trimmed closer to shell of the boot, meaning that the outer sole has a fairly narrow profile. Both of these factors have been shown to have a higher risk of the footwear 'rolling' when stepping on an unstable surface or piece of debris like loose rocks or uneven surfaces.
As the boot begins to roll, the boot carries the foot with it, the higher material of the boot above the ankle exerts more force against the foot to make it roll with the boot. That material is not stiff enough to keep from flexing, which means that your ankle is going to start bending as the roll of the boot continues. And because the foot is higher off the ground inside the boot, the ankle can be forced into a more significant bending.
Another factor about boots that helps lead to injury is their weight. The heavier the weight that the foot and lower legs need to lift, the more stress and fatigue the ankles and supporting structures are exposed to. Such weakens the ability of the ankle structures to maintain resiliency.
Trail shoes and trail runners, on the other hand, do the opposite when confronted with the same type of uneven surface or debris. The outer and midsoles are much closer to the ground. They are also wider than the shoe making for a contact point with the ground that is more stable. Their much lighter weight keeps ankle structures from fatiguing.
Now here is the thing researchers found as most significant: A foot in a shoe that is kept a bit loose can compensate, to a large degree, when the shoe starts to roll off of an uneven surface. As the shoe rolls, the shoe tends to slip
around the foot. In other words, the shoe moves around the foot for the most part, so the ankle won't immediately bend out of place with the shoe. This allows the wearer of the shoe to have enough time to react to the rolling and twisting shoe to keep the ankle from injurious strain.
Yes, there are people who get ankle injuries in trail shoes and trail runners. But those injuries are less frequent and less severe, on an average, than with a foot encased in an above the ankle hiking boot.
As stated above, there will be any number of folks that, with no predisposing medical conditions, will state anecdotal evidence along the lines that they, or a friend, or other family members, et al, were saved by above the ankle boots. Subjective opinion is like that.
But objective evidence begs to differ on the best way of protecting ankles and the lower leg structures.