We are usign combined method to get best of two worlds:
We use SSIS to get data from external sources and load it in parallel into Staging database
Then we use SSIS packages to orchestrate pipelines and trigger appropriate SPs inside control flow.
Any transformation logic is incaplulated into SPs as data flows are hard to manage/modify and doesn't give any significant advantage:
1) It's easier to modify and troubleshoot SP than a package
2) There's no way to easily reuse components in SSIS except calling external packages
3) SVN diff of SP works, diff of SSIS package is awful :)
Also, we use SSIS to run SPs in parallel to boost overall performance.
