Don't mind it? Hell, that's a big plus.
Best place? That depends on what you like.
The reefs all along the Keys are pretty similar. There are shallow reefs and deeper reefs. There's a wall (not a true wall, more of a very large ledge) running the length of the Keys. The reefs are not as lush as the Caribbean, but parts of them are excellent. You will see dead coral (a result of the screwed up ecosystem in the Keys AND on the Florida mainland. There are also lots of wrecks along the entire length of the Keys (deep & shallow). Some are screamers, other are artificial reefs.
Key Largo is crowded with divers, as you go farther down the chain, you are usually on less crowded dive sites.