Treat others as they should be treated. This includes patent examiners – many of who do a fantastic job. Be respectful to an examiner, but don’t let an examiner disrespect your client.
Patent prosecution strategy is complex. At least, it should be complex. If you are hanging on to hard and fast rules regarding appeals, interviews, citing case law, or being aggressive in a response, you are not doing your clients any favors.
If an examiner’s explanation in the Office Action of a rejection is difficult to decipher – examiner, you are not doing your job. And I’m not going to let that negatively impact my client. This is especially truein egregious circumstances.
There is a clear expression of the minimal requirements of examination in 37 CFR 1.104(c)(2):
“In rejecting claims for want of novelty or for obviousness, the examiner must cite the best references at his or her command. When a reference is complex or shows or describes inventions other than that claimed by the applicant, the particular part relied on must be designated as nearly as practicable. The pertinence of each reference, if not apparent, must be clearly explained and each rejected claim specified.”
If you think making this statement decreases your chance of getting an allowance, you are wrong. According to data I gathered from LexisNexis PatentAdvisor, I have made this statement in 9 applications that have been disposed, and the allowance rate is 100%.
The Examiner is not going to hold a personal grudge against you if you call out the blatant deficiency in an Office Action. The Examiner is not going to refuse to allow your client’s application if you say “Come on, this is a bad Office Action! You are not even trying!”
As long as you are calling the Examiner out using the MPEP or 37 CFR – the instruction manual telling examiner how to do their jobs. I will repeat that – as long as you are calling the examiner out using the MPEP or 37 CFR (or case law), it will not cause an examiner to play hardball.
However, there are caveats – don’t do it unless your client is completely onboard, it seems to be part of a pattern by the examiner, and you don’t think an examiner interview will help.
The stats from PatentAdvisor agree. I did a search using “pertinence of each reference, if not apparent, must be clearly explained” in Responses to Office Actions that were disposed since 2019, and here is what came back:

Calling out the examiner’s lack of explanation does not hurt your allowance rate…it might actually help, unless you are 3600, which has to be skewed by the business methods art unit. If you are dealing with an examiner in business method units of 3600, you should be as differential and polite as possible, because the examiner feeling bad for your client is probably the best route to an allowance.
It is not all positive. Calling out the examiner might draw out prosecution, as shown below:

In every tech center, calling the examiner out with “pertinence of each reference, if not apparent, must be clearly explained” in Responses to Office Actions causes more office actions to be issued than average. Thus, it might be more advantageous to interview with the Examiner.
However, what if interviewing is not a helpful option? For whatever reason – a client against interviews, an examiner who is not persuadable in an interview (some examiners’ allowance rates drop with an interview) or something else – an interview might not be a great option. See below what happens for applications where there is no interview. Does calling out the examiner help? YES!

Thus, do not definitely rule out telling the examiner to explain how the hell the examiner is rejecting the claims in view of the prior art. Prosecution strategy is never black and white. Keep this option in your arsenal, even if it should be reserved for special occasions when the examination is not living up to bare minimum standards.