Aside from the obvious fact that replacing the Stdlib with Base would break existing code, Base has an unstable and quite opinionated API and isn't tested on all targets OCaml supports (Jane Street is looking to drop support for 32-bit targets altogether). There would be a lot of tension to adopt it.

Meanwhile, the built-in Stdlib finally started to acquire much needed functions and modules during the late 4.x releases. My biggest worry is whether they'll keep up the pace, it doesn't even have a resizable array or, alternatively, a Clojure-like vector (but neither does Base).