I have the misfortune of having one foot that is a 9EE and another that is a 9.5E, so no matter what I do, one foot is always uncomfortable - usually its the short, fat foot.
Anyway, I tried Sidi, regular and megas. The regulars were too narrow and the megas were too wide.
I am now riding Specialized Pro Carbon shoes, which come in narrow, regular and wide widths. I have them in a 44 wide. They fit my 9.5E foot fine, but the short, fat foot, not so much.
After these, I'll probably try the Shimano wides.