More granularity for staff permissions
I think there needs to be some more granularity in user permissions. As a bare minimum you should be able to restrict staff to either the Payables or Receivables sides of things, like QuickBooks Online does, but honesly that's really not granular enough.
Better yet, one should be able to restrict what functions each user can get into (like Freshbooks does). For example you should be able to create a user who can enter invoices, receive payments, lookup and create customers, but not do anything else.
Example 1: Permissions in Freshbooks - http://community.freshbooks.com/support/how-do-i-set-my-team-and-clients-permissions/
Example 2: Permissions in QBO - http://quickbooksonline.intuit.com/screen_permissions.jsp