If I'm not in waders I still wear wading boots with neoprene gravel guards because it suits my need for foot protection on the high gradient stream that I like to fish. That said, I fished with a guy over this summer who wet wades all the time and has tried lots of different options. He said that he finally found the right wet wading shoe, the Riprap by Simms.
RipRap Shoe - Footwear - SHOP
I think getting debris of some sort inside your shoes or boots is pretty much unavoidable. I mean even when wearing my waders, using gravel guards and wading boots I find gravel on the inside.