I like a wider toe box and have very flat feet. So flat, that I wore custom orthotics for years as a child. Didn't do any good and I still have pain in the arches and get hot-foot while cycling sometimes. I've been very happy with Shimano shoes- and found that for me, a stiff sole makes it more comfortable as the sole isn't flexing when I push down. So I use their fiber soled shoes and just love them. Used to love Sidi but maybe my feet got wider because I find them narrow and constricting now unless I wear very thin socks.
I did find a really good (for me) moldable insole, made by Louis Garneau, that you put in the oven to soften, then put in the shoe and stand in them till they cool, and they mold to your feet. I put them in my Shimano mtb shoes and it is a perfect marriage; I have ridden in them all day every day for a week in Oregon on vacation earlier this month and my feet just felt great. I put the Specialized BG footbed in my road shoes and they help, but the LG moldable insoles are awesome.
Good luck finding a setup that works; it's like finding 'the one' saddle. The payoff in pain reduced/free riding is worth the hunt.
Tzvia- rollin' slow...
Specialized Ruby Expert/mens Bontrager Inform RXL
Specialized SWorks Safire/mens Bontrager Inform RL
Giant Anthem-W XT-XTR/mens Bontrager Inform RXL
Fuji Newest 3 commuter/mens Bontrager Inform RL
Novara E.T.A commuter/mens Bontrager Inform RL