I've lived in the land of stored procedure ETL for a multi-terabyte SQL Server data warehouse. This decision was made back in 2001 when .NET was 1.0, so VB6 was the programming language alternative, and SSIS wasn't around yet - it was DTS. I can tell you that there were advantages and disadvantages, like anything.
Some considerations:
- If everyone on your team understands SQL, it's easy to dig into the stored procs. SQL is a widely known skill which may be a benefit if you have a lot of ETL writers/readers. You have to be more than a casual user of SSIS in order to understand what it's doing. The high level graphical flow is nice for documentation, but if someone needs to get into the guts, they'd better know SSIS well.
- SQL is a pain to modularize. If you use UDFs, you are going to incur a huge performance hit. You'll write similar code in multiple places and you'll hate yourself for doing it, but often in ETL scenarios performance is king. SSIS will help you modularize and factor out your tasks.
- Don't expect to be able to easily use source control with SSIS. SQL - no problem. SSIS uses awful XML files which can be checked in, but good luck diffing with previous versions to see what changed and when.
- You need to think about your SPs in a modular way, even though it's hard to make them as modular as you'd like. Use temp tables to chunk up your processing. Put indexes on those temp tables before you use them. Don't try to do too much at once. Comment everything.
- If you're using cursors, you're doing it wrong. Don't be afraid to chain in some external console app you wrote in the language of your choice to do some things SQL just wasn't cut out for.
BTW - after I left that company, they finally upgraded the database from SQL 2000 to 2008 and slowly moved from stored procs to SSIS. At my new company, we own SSIS but after using it we all agreed that our custom written .NET ETL is a better fit for our purposes. Everyone takes their own route. The decision has to balance maintenance and performance and the skill-set of your team and the skill-set of the job pool in your area.