Rising another 1000 feet and looking down on Bill Me Later and credit card-based online payment, I found little difference between the two from the customer's point of view.  A credit card is essentially an aggregated billing service.  Instead of receiving bills from all the merchants, the customer receive one bill from the card issuer.  One key difference is that  Bill Me Later doesn't use a shared secret (credit card number) as account ID.  With credit cards, you are forced to share that secret on every purchase with the merchant.

Technically, not much change is needed to adapt 3D-Secure to work with Bill Me Later.  With Bill Me Later, the ACS can handle payment on top of authentication and authorization, increasing throughput as well as making merchant side simpler.

Bill Me Later should take a serious look at 3D-Secure for several reasons:

1. Look and Feel – 3D-Secure UI will be what users will be expecting to see when they make online purchases.  With both Visa and MasterCard making efforts to make this happen, alternative payment methods should adopt similar look and feel to avoid startling the customers.
2. Merchant Adoption – Merchants have either installed 3D-Secure merchant plugin already or have plans to do so in the near future.  Slipping in Bill Me Later support into those merchant plugin will be simpler than asking merchants to install yet another software their servers.

Bill Me Later should work with 3D-Secure vendors such as Arcot Systems which currently has the largest 3D-Secure merchant installation base.