A known problem when storing time series data in HBase is having hot regions when using timestamps as keys. A common solution is to use a salt as prefix to distribute the data over multiple regions. This presents a problem when one wants to process the data ordered by timestamps in a Map/Reduce job, as currently only one Scan object can serve as input. One approach is to start a Map/Reduce job for each prefix.
More info: berlinbuzzwords.de/sessions/near-real-time-processing-time-series-data-hbase