You say "lowest common denominator," I say "subset of JavaScript." In fact, JSON objects are clunky to access in some languages, like C. JavaScript's lack of proper sets and maps is a weakness of the language's standard libraries and is in fact being corrected. It seems quite unreasonable to me to use JavaScript as some sort of Platonic ideal of a programming language, where anything that has a different feature set is automatically bad.
It's kind of a big leap to go from "This is not a strict subset of JavaScript" to "You're ignoring the web." If you really want to deal only with JavaScript-native data structures, I can't see any reason why you couldn't deserialize EDN into those. If you really like the added data structures in EDN and don't want to lose those in your JavaScript program, you could just use Mori or something similar.
