I recently bought a nice pair of shoe covers for cold (not cool) weather cycling. Heavy weight neoprene with opening on soles for spd or atac type cleats. Even though I have XL covers, I can't use them with mtb shoes because of the lugged soles. No problem I just put mtb cleats and pontoons on road shoes that had both 2 and 3 hole mounting systems.
Before I purchased the shoes, I looked in a bike shop and found that I really wasn't crazy about the shoe covers because they were largely open on the bottom with perhaps just a strap across the bottom. Now I realize that perhaps that might have been exactly what I needed for lugged soles.
What design features should I be looking for in covers to use with lugged soles?