Many times just as a sequence is started or after a few emails, the contact or lead is "out of office" and this if you use the end sequence if responds cannot be used because of this, limiting the usefulness of that great feature to pull out engaged/responders from an email sequence.
Suggest we need a way to Ignore auto reply in sequences (or give ability to filter response subject say ignore subject content entered eg starts with "XXX" like “Auto”); you are reading emails, creating suggested content/actions and we have filter capability to leverage.
One other idea lesser but doable is to create a task option for any response with easy click of button to either continue or remove that record from sequence in the list seeing some of the response subject/body.