Clearly separate automatic and non-automatic invoices, manage by service/client.
It seems like this would solve a lot of the problems mentioned in this forum regarding customer confusion about automatic payments.
As mentioned in this thread, with some extreme custom coding and unfortunate modification of the core files it's possible to sort of manage conditional language in the emails that let clients know their invoice will be automatically paid.
The problem is that when they sign into the client area, they still see an unpaid invoice with no indication that it will be automatically paid. This is less of a problem if it's a credit card invoice but for PayPal subscriptions the automatic payment will still come through.
WHMCS already lumps things into one invoice if certain criteria match (due date, payment method, etc). It seems like it'd be better to give us a checkbox for every product/service/domain in the client's profile (on a per-client basis) that would indicate whether that service is on automatic payments.
From there the system could treat emails and invoices for those things differently by default. There could be a separate set of emails for automatic invoices (as there currently are for credit card invoices), there could be a separate section on the Invoices page in the client area below the main list that would list automatic invoices, etc.
If it's possible for WHMCS to tell whether a PayPal subscription has been set up, even better. It could automatically check or un-check the box based on that, and give the client the ability to enable/disable automatic payments for recurring services/domains in the client area, which would automatically cancel the PayPal subscription if disabled, etc.
Just an idea but I would say that poor handling of automatic payments is one of the biggest areas of confusion for clients, and frankly I think for most of us, issues that affect customer experience take a much higher priority than exclusively admin issues.