You have to remember that this is actually how the FDIC works... When a bank is declared insolvent, the FDIC facilitates a purchase of depositors' funds to another bank or a group of banks. This is pretty standard.
The purchase of assets that are not depositors' funds (real estate, furniture, computers, etc.) are a separate transaction between JPMorgan and WaMu, and those funds will be used to pay down WaMu's existing obligations to creditors during the bankruptcy process.
Stockholder's are wiped out, as they should be, because when you buy stock you're investing in the future revenue stream of a company, which of course, there won't be any.