I use a set of Shower Pass Booties that are more like a poncho for your shoes than the usual neoprene type that are very difficult to get on/off. These
come on/off easily over my treaded mountain SPD shooes, and are pretty water resistant (but not waterPROOF). You do have to cut a hole for the cleat, and I do use an other elastic pant-cuff velcro strap at the top to seal off leakage, but they do the job and are far less frustrating to get over the shoe. The major downside is that you look like some kind of cycling elf with big, puffy feet.