I'm mostly concerned with using APIs that are only available in io.js. Doing so means I can't share my modules in any reliable way since io.js and node both use npm and I certainly wouldn't create multiple versions of my modules. This leaves me developing using only node APIs at which point io.js is nice for experimentation but I'm not sure about doing serious work for it until it's strictly an application (no module sharing, etc).
Really the biggest sticking point for me is using npm between the two. Node not supporting ES6 is also an issue as you can't write your code using ES6 unless you want to only support io.js or you want to transpile (ugh).