Thanks so much for the kind words and support everyone. Spriter itself and support for all of its features in C2 will only improve for a very long time to come...we've got lots of cool things planned for Spriter and it's C2 integration.. Thanks for your patience as we get there.
Last I knew, Spriter scon files work fine with cocoonJS exports so long as you have minify script turned off when exporting. Is there a specific problem you are having, perhaps on a specific mobile platform so we can troubleshoot the issue for you?
Mike at BrashMonkey