We have a work-around for the "Manual" option. We disable the option to pay manually, and then just make an identical Registration Type that is "Pay at the Door", which is set to cost = Free. A bonus of this option is that when someone completes the registration, their Status is automatically set to "Confirmed"....whereas when they select "Manual" on a PayPal option, the status is set to "Pending" until an administrator changes it.
The only thing I don't like about this workaround is that Free registrants get sent a different confirmation e-mail than the other registrants. It can actually be used to your advantage (by putting in a paragraph detailing how they can pay) but it's another thing that has to change event-by-event.
ETA: Another thing I don't like is that using this workaround gives users the impression that there is a way to get into the event for Free. This is the missing link we are talking about- the ability for it to say the Registration cost is $20 (for example) but they don't have to pay anything online.