The biggest inefficiency is the passengers themselves. It's amazing how many people can't be bothered to even read the stated rules ahead of time. I fly a lot, and I'm amazed how many still try to bring large bottles of liquid....hello.
The worst time suck though is the morons who grab their stuff right as it exists the x-ray and then stand there putting it all back on. This stops the conveyor because they haven't removed their bins from the belt, and the guy running it has to slow it down. Of course, 10 or 20 feet away there are benches and tables for people to move to where they can put their shoes, belts, whatever on. But no, stand right there and hold everyone else up..
I asked a TSA agent why they didn't tell these morons to pick up their bin, walk it out of the area, sit down, etc and he said they couldn't yell at people, but he encouraged me to yell at them. Great!