Clojure still uses S expressions, it just has more than just lists available. Square brackets don't make lists, they make vectors. Commas are always optional. I don't know what you mean by "arbitrary lists where pairs which belong together aren't grouped", but maybe you mean maps or sets, which are also not lists but a different data type.

  user=> (type [])
  clojure.lang.PersistentVector
  user=> (type '()) ; gotta quote the list
  clojure.lang.PersistentList$EmptyList
  user=> (type {})
  clojure.lang.PersistentArrayMap
  user=> (type #{})
  clojure.lang.PersistentHashSet

Different data types are used for different things. Vectors have more natural insertion behavior, so most people use them where that might happen.

  user=> (conj '(1) 2)
  (2 1)
  user=> (conj [1] 2)
  [1 2]

The example that most typifies my issues with Clojure syntax is let-binding. In Lisp it's very clearly structured:

  (let ((foo bar)
        baz
        (quux frob))
    ...)

In Clojure not only are the bindings unstructured, they are thrown into a vector. Not a list, not a map (for which Clojure has dedicated syntax, mind), a vector.

  (let [foo bar baz quux frob]
    ...)

And that is one of the only two places I know of where Clojure arbitrarily uses a vector when it uses lists everywhere else:

  (defn foo [bar] ...)

Instead of either of:

  (defn foo (bar) ...)
  [defn foo [bar] ...]