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Can you provide some additional details? Is this for an Enterprise Portal or HCM system? Enterprise Portal has the role based branding framework that you can use to change headers and footers. HCM does not have this feature. You can build something, but it would be about as supported as iframes, but a LOT more work.
How are you using iframes now (or how were you using iframes prior to the upgrade)? Is this in a specific component?
The only problem I have had with iframes is that I have to specify content inside the iframe. Whether I'm using pagelet wizard or just an HTML area in a component, I have to add an &nbsp; inside the iframe tag like this: <iframe... >&nbsp;</iframe> so that PeopleSoft doesn't strip the empty block element from the output.