I actually have quite a few gripes with Elasticsearch. It's a pain to manage - there seems to be no way of killing long-running queries other than restarting it (so if you have users using kibana etc at some point someone will submit a impossibly hard query and kill the server), the quality of the search results just isn't that good and it takes a lot of customization to improve it - I've never been impressed with the results from any of the large deployments (e.g. github). Ideally it would come with good tokenization and synonyms etc out of the box rather than every deployment having to tinker with settings until it seems to work.

That said ELK is great overall and I would still use it for user-facing search, but I think there is still a lot to improve.