My biggest wish is for the ClojureScript compiler to be less accepting of stupid code. I've made all kinds of moronic mistakes[2] that would ideally yield a warning or even a straight-up error, right at the source, but they don't and I just end up finding data structures full of nils at runtime. I've also hit a few traps with lein-cljsbuild[3][4]. This is all definitely improving though.
I've now started my first real Clojure project, a web app built on Luminus[5]. Luminus kind of strikes me as training wheels for Clojure. It's easy to get started with, and minimizes the sense of foreign-ness coming from a Python web development background. But I doubt I'll still use it once I have more experience, as opposed to simply putting its component libraries (Compojure, Ring, lib-noir, etc.) into a project directly. Which is fine; it fills a valuable role in the ecosystem anyway.
1. https://github.com/graue/dumbbell
2. Example: http://dev.clojure.org/jira/browse/CLJS-639
3. https://github.com/emezeske/lein-cljsbuild/issues/239