Looking at options for embedding the 3D Secure page inside my own order form, I came across the following:
\"Some commerce sites will devote the full browser page to
The only reasons I can think of are actually in the wiki article you referenced to mention a couple...
"The "Verified by Visa" system has drawn some criticism, since it is hard for users to differentiate between the legitimate Verified by Visa pop-up window or inline frame, and a fraudulent phishing site."
"as of 2008, most web browsers do not provide a simple way to check the security certificate for the contents of an iframe"
If you read the Criticism section in the article it details all the potential security flaws.
Otherwise the only difference is the fact that an IFrame is an inline frame and a Frame is part of a Frameset. Which means more layout problems than anything else!