Although you cannot completely eliminate these recovery/comparisons at the 
moment, there are some things you can do today that may help. If you go 
through this presentation, it talks about some settings on when ES should 
start recovery after full restart:

http://www.elasticsearch.org/webinars/elasticsearch-pre-flight-checklist/

It is also possible to disable allocation before shutdown and then 
re-enabling after you are fully back up. 

And in the future, there is current work that is being done to make this 
recovery process more efficient (see short description about Sequence 
Numbers):

http://www.elasticsearch.org/blog/resiliency-elasticsearch/

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