I had been suffering from the exact same pain and fatigue problems and I tried everything from multiple bakes, Superfeet, heel lifts, R-Fit, even custom insoles along with trying to correct a pronation problem. None of it worked, in fact everything I tried made it worse. The pain was sometimes so bad i'd have to take my skates off, let my feet breath for 5 minutes and put them back on. Loose laces, tight laces, didn't matter, I had bad foot pain on the bottom of my feet from heel to balls. As a beginner 8 months ago I didn't know the first thing about skates and proper fitting so I relied on the guy at the LHS where I purchased my skates. Looking back now, I have a very strong feeling the guy was just trying to push the skates I was trying on because a week after I bought them they went from $389 to $209, an no, the guy didn't want to hear it when I went back a week later to complain about this and the pain I was having. The skates I bought were Bauer Supreme S27 7.5D's. I asked about others like Vapors and CCM's but he just kept saying nah this is what you want. A newb I trusted in his opinion. I'd had enough and through reading many posts on here and elsewhere I was convinced the skates were the wrong size. Now that i've got past the walker stage and am able to play a bit of hockey I figured i'd go elsewhere and try on every skate I could and try to get a better fitting. Anyway, I went to Monkey Sports in Woodbridge NJ and I can't give these guys enough props. They put me on each of the scanners, both Bauer and CCM, 3 times. The Bauer came up with Vapors 7EE as the recommended skates, not Supremes. CCM came up with 7EE jetspeeds. I tried them both, very nice, but I wanted to try on every goddamn skate they had and I did and the guy I worked with was more than happy to let me. He manually measured me a couple of times as well. I nailed it down to Vapors and Ribcors, both 7EE. The guy said lets bake them and see before you decide. They baked them! I hadn't even paid any money yet! Great store. Anyway, I ended up getting the Ribcor's. They were so comfy like a fluffy bunny slipper, and after the guy baked them and I sat in them for 20 minutes then walked around for 10 minutes they were unbelievably comfy. I also chose the Ribcor's over the Vapors because of CCM's 90 day policy, because who knows how they would feel after being on the ice with them for an hour. At least if I skated with them for a week and didn't like them I could just return them and pick something else. I have had zero pain in the Ribcors and have skated in them endlessly, they are as comfy now on the ice as they were in the store and it has made a world of difference in my skating.
The conclusion to this longwinded explanation is that the 7.5D Supremes I had were too narrow for my foot and were therefore squeezing the sides of my feet together which was causing pain on the bottom of my feet. Putting in supported insoles like Superfeet and the custom insoles I wasted money on were just making things worse because they were pushing up the arches of my feet and exacerbating the pain from the sides of my feet being squeezed by a skate that was too narrow for my foot. I now use superfeet insoles in my Ribcors because I like the bit of heel lift it gives and my feet are absolutely pain free and my feet do not get extremely fatigued after 20 minutes on the ice.
So when I hear someone talking about foot pain like this the first thing I have to say is, it's a skate fitting problem. Not that i'm an expert, i'm just a beginner, but i've suffered through exactly this problem. And I'll go nowhere else except for Monkey Sports from now on when I need skates.