Plot holes and logical inconsistencies that are deliberate design decisions remain plot holes and logical inconsistencies. For some people, and some movies, they work. For some people, watching certain movies, it's jarring.
For example, I'm not going to question why an air traffic controller like Johnny, making his pterodactyls out of weather reports, hasn't been fired yet. I'm not going to question why the autopilot's a blow-up doll. I'm not going to ask what sort of nervous disorder makes a guy miss his mouth every time he tries to take a drink. And I'm definitely not going to ask why everyone keeps calling the doctor Shirley. For a movie like Airplane, which doesn't have a single serious moment in it, and never pretends to be anything else, it works.
However, I feel Pacific Rim should be held to a different standard. Saying "This doesn't make sense, but that's okay because of Rule of Cool" is fine and well. But unfortunately, I can't turn off my logic filters quite so easily, especially since Pacific Rim is so much more serious in tone than farces like Airplane.