Don't use the regular "'submit by email button." If you use this button, you can only submit the data as XML. Instead, make your own button.
In the Object library under Standard objects, click and drag a plain button to your form. Change the Control Type to Submit. Now you should have a new tab called Submit with a "submit to URL" option. In that field type the return email address in the following format: mailto:jdoe@domain.com. Toward the bottom of the same option, there is a field that says "submit" and the choice is XML data package. Change that to PDF. Then change the name of the button to "Submit by Email." Now when you preview your form and click the Submit by Email button, it should mail the completed form as a PDF instead of simply mailing the raw data.