First of all appologies for replying so late. In my opinion for any ETL based queries Athena does not seem fit to, because the computation is something that can't be controlled by us, its AWS managed. So if you have long running ETL jobs performing heavy processing of data, then I would prefer EMR or if you want to avoid cluster management then AWS Glue also is a good option. AWS Athena is more for Ad-hoc query and analytics.