Love your well thought out feedback.
1) IMO ES5 is highly available now and when it isn't you can use shims.
2) Will definitely add other module systems on request. Currently works in the browser with browserify.
Isomorphic JS is only going to get bigger. Writing browser-friendly modules in CommonJS is an admirable strategy, especially since you're trying to avoid requiring your own custom build system.
I use Webpack (similar to Browserify, but I understand Webpack's more powerful), and I can't imagine starting a new JS project without it.
