I have what is considered a normal foot size, and I could not get my right foot comfortable in my Nike's. Just last week on (the Pedal / Shoe Thread) I was complaining about the same thing. Today, on a long ride, both shoe's felt great. I guess in my case it was just a matter of breaking them in. I don't think it's a width issue either, as I can move my toe's around, and the sides are not bulging out even when I'm standind in them. I'm glad I don't need to go looking for another pair now, because I love the stiff plate on them.
I just hope you find shoe's that your happy with. That is the overall most important thing.