I've been pretty intensely researching this stuff so I'll throw in my $0.02
Booties: best for sand, grass, sporadic coral flats. Do not use on coral reefs or shell bed flats (sole is too thin and will wear out in one trip). Great for the "permit at 100ft, throw your booties on and jump out" shots. Patagonia booties - v nice boots, but fit narrower, tighter up top and lets less gets in, sole thinner than simms Simms booties - wider, best fit for my foot, thick sole but ankle is more loose than the patagonias which would allow material to get in. would wear socks inside these if I had them
Shoes: Only for coral or sharp bottom wading. not recommended for boat to flats transitions. OK for all day sand flat wading but get heavy.
Given all of this.. I had low top water shoes from previous trips and I bought MEC neoprene sock booties and wore that combo in Belize/Mex. Worked fantastic and didn't allow any sand in the high top neoprenes. It was a good temporary fix, but I'll need better footwear for the next trip