I just discovered a couple differences in the way SQL Management Studio (SS2005) creates change scripts versus Enterprise Manager (SS2000). The first is that SS2005 places a GO statement after each BEGIN TRANSACTION. SS2005 also replaces 'user' with 'SCHEMA' for level0type when calling sp_addextendedproperty. I'm not exactly sure what the first one accomplishes, but I imagine the second one is because schemas mean so much more and are so much more useful in SQL Server 2005.
That reminds me, what happened to the 1992 versions of SQL Server that should have been between SQL Server 7.0 and SQL Server 2000?