Alex Feinberg answering the question in the title:
This is like saying “how does a General Motors bus compare against a Ford engine”. MegaStore is built on of Google’s BigTable/GFS. HBase/HDFS are BigTable/HDFS work-alikes.
BigTable and HBase give up availability (in the CAP Theorem sense) in favour of consistency: when a tablet master node (HRegionServer in HBase) goes down, the portion of the keyspace the failed node is responsible for becomes (briefly) unavailable until another node takes over the portion of the key space. This is efficient, as the data/write-ahead-log is stored GFS (or HDFS): in a way serializing writes to GFS/HDFS (a file system with relaxed consistency semantics) through a single node ensures serializable consistency.
Make sure you read it all.
Original title and link: How Does Google MegaStore Compare Against HDFS/HBase? ( ©myNoSQL)