Nice topic! I've been reviewing permit applications for stormwater, septic systems, wastewater treatment plants, water quality certificates, injection wells, and just about anything else water-related (plus landfills and NEPA environmental review) for 11 years now. I've narrowed my technique to focus on big-picture issues first (will the design work, and does it meet the intent of the rules) and the nitpicky stuff last, which most of the time I don't even bother with. My attitude is that the design engineer is ultimately responsible for the fine details of the project - my responsibility is only to make sure he has satisfied the requirements of the regulations, and his design won't hurt anyone else.
I have some designers, who I respect a great deal, that get along well with me and have even served as my reference for the PE exam. But there are plenty others who don't like me very much at all. For the most part, they are the under-qualified engineers or the clientele of the rubber stampers, so their animosity doesn't bother me too much (their goal is usually to get around every regulation they can, anyway, because compliance is not their business - they are usually the construction contractor and just want to start building). I often get more nit-picky with them, because they do such poor work anyway, I hope that they learn something from the process and try a little harder next time. Some of them do, and have (over time) developed better relationships with me.
And then there is a small number of experienced engineers who object, on principle, to having anyone else review their plans ("I'm a PE! You can't question me!") Those guys are the biggest pain in the ass because they often refuse to make changes, and the only way (as a regulator) to deal with that is continue to send them the same deficiency list over and over, which they then use as proof (to your boss, the local politicians, etc.) of how "unreasonable" you are. Regulations (and the laws of physics, sometimes) simply do not apply to these guys - they know it all, and the regulation/equation/book is wrong.
The biggest lesson I have applied over time is to always suggest a possible solution to each deficiency noted. That does two things for you: One, it helps the regulated engineer learn what the regulations expect of them, and two (most important?) it gives you a great "out" when some sleazy local politician comes for your head on behalf of one the the "bad" engineers - almost without fail. "But I told them how to fix it!" "Three times!"
But I am sick and tired of the whole business. It really wears you down. I am actively looking to move on, and get away from permit review work.