This is a huge question! I've been hiking and climbing for a long time and I've learned a lot of things about shoes.
#1 get the pair that fits best.
Every shoe/boot manufacturer uses a different "last" which is the generic foot shape they use to make the shoe. So what boot fits one person might not work for you. Thus you cannot take any brand recommendations based on fit. You can take recommendations based on durability though. Boots like limmers are the top end of bulletproof boots, with about a 5 year wait for a custom pair.
Definately go with Vibram soles.
I have a pair of shoes/boots for every occasion. One pair can't do it all for me unfortunately. My personal preference is for the lightest shoe possible. Not everyone will agree, in fact most people will think I'm stupid. But these are also the same people I pass on trails carrying 60 pound packs while mine weighs 25.
The old adage "a pound on the foot is 5 on the back" is absolutely true. Out here in Colorado I do a lot of hiking, scrambling, climbing, bagging fourteeners, etc. So I'm navigating nasty terrain, up to third class with a max load of about 30 pounds. I like to feel connected with what I'm stepping on. Wearing a big boot hinders my feel for the terrain. And after the day is done I rarely have any foot problems.
Ankle support is a myth. I have twisted my ankles just as bad if not worse in hiking boots than with low tops. If anything the fatigue you get from lugging huge boots around makes you more prone to ankle twisting.
Stock insoles are crap. Toss them out and get something good like superfeet or one of the custom molded kinds out there. It is funny how we spend so much time on our feet but fail to take care of them.
Don't buy a pair of leather boots and expect to wear them the next weekend on a backpacking trip. Your feet will suffer. I don't know how many countless people I've sold boots that were going to hike the Grand Canyon "this weekend" and came back to return the boots due to blisters. I'd just think "buddy, your an idiot!" Good leather boots don't break in, they break you. Sometimes boots need to be resoled before they feel really good.
Best advice is to try on a LOT of boots/shoes. Go with what fits best. Pick a pair based on conditions. In Arizona , get lots of mesh. I'm Michigan, get something waterproof.
Oh, and pick up a pair of gaiters too.
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