I get ragged on a lot about it, but I simply choose not to go with a cleated pedal setup.
With that in mind, I encounter rainy weather from time-to-time and as often as I equip myself with the proper pants and jacket, I never find any neoprene shoe covers for regular shoes, even the largest ones are still formed to fit over cleats for whatever reason and do nothing to keep my shoes dry.
Aside from those aqua-socks, I'm wanting to find something that's already available as opposed to "making something from scratch, all ghetto."