Documentation shows that Redis output is deprecated, and I didn't see Kafka at all. Is there an architectural reason why I would not want to use a message queue between Beat and the Logstash indexer? Are there any plans to support message queues in the future?
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We still recommend the use of a broker, at least until the next major release of Logstash that will contain one.
I'll let the Beats team comment more 
I would be very interested in either ActiveMQ or EventStore protocol support for packetbeat. I guess this comes under this topic.
Best is to have a look at the discussion here: https://github.com/elastic/filebeat/issues/132
@megakid If you refer to packetbeat supporting to read these protocols, I think this goes into an other topic. Here is a list of requested new protocols: https://github.com/elastic/beats/labels/new%20protocol