Unpredictable response times since upgrading from 2.4 to 5.1.2

We've (in place) upgraded from 2.4 to 5.1.2 and since we get sporadic slowdowns with simple document GET queries.
Aggregating a specific query type for the same day with the old 2.4 cluster and the upgraded 5.1.2 cluster yields the following numbers:

N           Min           Max        Median           Avg        Stddev
 x 80801      0.433811     28338.847      1.481119     321.63365     1296.8558
N           Min           Max        Median           Avg        Stddev
x 78746      0.479862     383.48786      1.411027      2.259211     6.7429293

ES2 has an average response time of 2.25 ms with a max of 383 ms, while ES5 has an average of 312 ms and a max of 28.3 seconds...
What's strange the median looks OK, but there are some very slow queries.

Apart from the 2.4->5.1.2 server (and 2.x->5.x java client) upgrade , nothing has changed in the cluster.

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