JavaScript has prototypes for a reason -- use them. By using the "module" pattern to build objects, you create a separate copy of every function for every instance of every object you create. If you're just creating a handful of objects, it's no big deal, but if you're creating a large number of objects, it's horribly CPU and memory inefficient.
Modern JS runtimes like Chrome/V8 can create and store a million small objects with prototypes and "new" in a couple seconds, using just a dozen or so megabytes of RAM. Creating the same million small objects with the "module" pattern takes minutes, uses many hundreds of megabytes of memory, and often crashes the browser.
And that's just the pragmatics -- there are deeper semantic reasons to use real prototypes.