I don't think I've ever ran across a situation where I've needed STM. Most of the time you can just use pure functions, and when you absolutely need state, an atom is usually the best tool for the job. STM strikes me as a very specialised tool, at least in the context of Clojure.

I don't think metadata is a bad idea. It's data about data. As long as you don't assume something will have the same metadata as the data it's derived from, you should be fine. I don't necessarily like the way Reagent uses it, but it's not out of character for Clojure to use metadata semantically.