Hi Jayme,
I was having a very similar problem. Though it was with queries and not filters.
You could have a look at "query_cache" property in _nodes/stats?pretty=true for both 2.0 as well as for 1.3, if you are seeing any differences there. (https://www.elastic.co/guide/en/elasticsearch/reference/2.0/query-cache.html)
You can try tweaking the cache size, to see if that solves/ reduces your problem.
In my case, the "query_cache" was being used even though the queries were not being executed as a filter. And the miss count was quite high.
More details : Search is slower in ElasticSearch 2.0.0 than 1.7.3 when the document count is high ( > 2.5 million)
Unfortunately, I do not have any more information on this. Hopefully an expert can throw more light on these issues.
Thanks,
Vignesh