Here's a couple of features that I have noted to be missing from whmcs.
1. Separate billing contacts for each webhosting package. This is very important for users that represent several companies or private customers. They could buy the webhosting packages under their own client accounts but still get the invoices with the right information.
2. PDF invoices attached to due emails. This is very important especially in the case where there is a fee if the invoice is due too long. I have noted that 90% of the customer pay using the last PDF invoice they have. Since the system does not send a new PDF invoice after the overdue fee is added, they never pay it.