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No. The main motivation behind a migration from IPv4 to IPv6 is the increased pool of available Internet addresses. We're eventually going to need to switch to IPv6 for the same reason that much of the U.S. now uses ten-digit dialing for telephone calls: we'll simply run out of addresses.
The security benefits of IPv6 (namely, IPsec) are all available in IPv4 as well. No feature of IPv6 will hinder malware's ability to affect an organization. There really isn't a good justification for moving an organization to IPv6, unless you want to stay ahead of the technology curve.
For more information on IPv6, read my advice on whether IPv6 would improve network security in your organization.
More information:
At last year's Black Hat Conference, Vista users were urged to beware of IPv6.
Teredo allows internal networks to transition to IPv6. Ed Skoudis explains why that's not as innocent as it seems.
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