There was no difference architecturally in SSIS 2008 and SSIS 2008, and there is no difference or enhancements in SSIS 2008 and SSIS 2008 R2 version except one. In the ADO.Net destination adapter, an additional property has been made available to bulk insert records when possible. And probably this is more of a move to support inserting data into SQL Azure. I had authored an article on the same subject which can be read from here. Those who are keen to learn difference between SSIS 2005 and SSIS 2008, check out the "SSIS New features in SQL Server 2008" series from here.
Theoretically, when you consider migration there should not be any issue between 2008 and 2008 R2, and I was under the same impression too. But as Einstein said, "In theory, theory and practice are same, but in practice they are not". Recently there was a migration issue reported on migration of packages from 2008 to R2, but this issue is limited to ADO.Net destination adapter control only. And just by modifying the XML of the package, the same can be resolved easily. John Welch explains this issue and the solution to the same in a very elaborate manner, which can be read from here.
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