Point 1: You will almost always be transpiling your javascript. In any serious project, you will want to have lots of small files to ease development, and then concatenate into larger files to ensure optimal http loading. If you don't already do this regardless of modules, you probably should.
Point 2: If you are intentionally or serendipitously relying on script execution order, that is your bug. The module loader has helpfully exposed a bug in your code for you.
Point 3: If you have lots of modules, it is simpler to deal with a module system than mashing together a load of scripts.
This complaint should come with a severe disclaimer that it only applies to trivial applications, because as soon as you start building something complicated the arguments are just plain wrong.
Software engineering is hard, and robust software engineering practices usually only pay off once you get beyond trivial examples. The ones that work, however, pay off massively once you do use them for more complex use cases.