I'm starting to read into the technologies in this area (i.e., I have not used much of the Hadoop stack yet), and I haven't found a fundamental reason why one would not base their batch processing on S3 (or your object store of choice). Existing software appears to make assumptions about the storage medium being a local hard drive.
Much of the challenge of HDFS appears to be around scaling the NameNode, and provisioning capacity. S3 dispenses with these issues, and the only cost appears to be throughput.
If software like Spark was modified to have a much more native approach to S3, could HDFS be dispensed with entirely?
[1] https://blog.twitter.com/2015/hadoop-filesystem-at-twitter