Currently, it is impossible to influence the order in which the "Modules" show up in a generated site's menu when including them like this in the site descriptor:
As far as I can tell, the order of items in the menu depends on the order in which Maven builds the modules – and this does not always put the most important module at the top of the list. In fact, the top of the list is in all likelihood occupied by various low-level infrastructure modules; the high-level, user-visible modules typically come much later.
This also means that the order of menu items depends on the module's dependencies; thus, this can result in unforeseen changes to the site when one module's build changes. Why doesn't Maven simply use the order of the module elements? That would be simple and predictable.