I learned long ago that to keep my feet in comfortable mode, especially if walking a long way, I needed inserts. The choices as I came to understand it is between inserts for cushioning (e.g. Sorbothane's) and inserts for support (e.g. Superfeet) and I've bought both. My preference is to use my Sorbothanes for hiking and the Superfeet for running. I could use them the other way around but from trial and error that is what my feet like best.
I also carry the original boot inserts with me bacuse I get to the point sometimes, again on a long hike, where my feet and the Sorbothanes are just too hot together so I chop and change improve my situation. I often take the Sorbothanes out and put the original inserts back in for a while, this creates a bit more space in the boots which for me can ease discomfort. Sometimes I do this because my feet feel swollen from the effort of the day, not by much but enough to know that I need a bit of toe wiggle room for a while.
I personally also prefer to hike with soles that are more flexible and I know that there is a school of thought that suggests that some people prefer to hike in trainers, expecially off road trainers. I could be persuaded to do this, sounds a good idea (without a rucksack) but I hesitate to do it because I'm just not sure how my feet would cope over days knowing that I have a 48L rucksack on my back.