Like fransisco said, you can seperate your code easier. I mean, if you instantiate all your widgets in your JavaScript code, your JavaScript will become pretty large and your HTML will usually be small (only contains "container" nodes which you use to place widgets in).
Better performance: I have to agree with you that it indeed lowers the performance since you have to parse your entire page, but you can optimize that by disabling parseOnLoad and by only parsing the DOM nodes you actually need. At the company I work for we did that by placing all Dojo widget markup inside a <div> with a certain classname. Then in our JavaScript code we do something like:
query(".containsDojo").forEach(node) {
parser.parse(node);
});
No switch between HTML and JS: The switch between HTML and JS makes it easier to understand your code and to have a context. For example, if you need to modify widget A by widget B that's placed on a page called C.html. Then it's easy to look for your widget A since you know on what page it is and where it's located (top, bottom, ...). If you put everything in your JavaScript file, you will have a hard time managing your code since you don't know in what context the widget is initialized. You will have to look through your entire JavaScript code because the widget can be initialized at any point in your code.
Easy to dynamically change the content: If you need dynamic content I usually create some kind of widget myself and put the JavaScript logic there so my "main" JavaScript and HTML code still look clean. You can always use the dijit/registry module to change certain things in your content.
Easy to read and be maintained: I totally disagree with that, similar to what I said in my previous paragraph about the switch between HTML and JavaScript. I mean, what's the difference between a dijit/form/TextBox and a normal HTML input-field? Not much, they're both UI items. Yet, if I follow your thoughts I would put the TextBox somewhere in the JavaScript code and the normal HTML input field inside your HTML. The HTML not only provides you a context, but also centralizes all UI elements.
