I like Jhon's idea :P
I use thin wool trail running socks, either defeet or smartwool,(for some reason, I havent had as much smell problems after switching to wool socks instead of synthetic) combined with super breathable trail running shoes. (my pick: salomon XA pro 3D)
also, whenever I take a break for longer than 5 mins, I take off my shoes and socks too let them breathe. the lacing on the salomons is nice because IT is fast to tie and untie.
the thing about mesh shoes is that it does allow some dirt and dust to get in (keeps gravel and mulch out) It is in some ways nice because it gives you a reminder that you need to clean your socks and feet (I try to do this at least daily) when you might otherwise forgett
the best thing for your feet, as far as avoiding fungus and smell, is to keep them clean and dry, and whenever possible, give them oxygen (leave the goretex for the snow only)