I don't see much changes in modules.require vs System.import, except in AMD dependencies can be file names.

But there are some differences in define:

modules.define(
  {String} moduleName,
  [{Array.<String>} dependencies,]
  {function (
    {function ( resolution, [{Error} error] )} provide,
    {Array.<*>} ...imports,
    [{*} prev]
  )} declarationFunction
);

What if we will compare dependencies.length with declarationFunction arity and decide with mind on that how to call declarationFunction?

It will help us to use modules as AMD module loader.

Is there any other problems or differences between current ym functionality and AMD standard?

Why I ask? Because ES6 modules comes to us. And I think about using ymodules for ES6 modules.