There's often lively discussion on this issue at MSF.
The keep-it-in-first camp says: maintain readiness to pull out quickly in an emergency. The keep-it-in-neutral camp says: avoid the hand fatigue and avoid stressing the bike's components.
Safety often involves weighing many potential risks, and waiting at an intersection requires a rider to think about several. A major research study showed that 3.2% of motorcycle crashes occurred when a motorcyclist was struck from behind; certainly not a major cause of crashes, but still a factor to consider. One point for the keep-it-in-first camp. But consider that if the light turned red just as the rider approached, the rider would have to hold the clutch in for up to two minutes or more depending on traffic and the timing of the signal lights. One point for the keep-it-in-neutral camp. If a semi-truck pulls up and stops behind the rider, the truck offers some protection against a drunk driver barreling up from behind, but the truck driver might absentmindedly start moving as soon as the light turns green, and forget that the rider is there below the driver's sight line. One point for each side.
A rider should be constantly aware of what's going on all around. What are the traffic conditions? Is it daytime or night? How well can you see to the front, the sides, and especially to the rear via your mirrors? Do you have an “escape path” in mind? Where we net out on this one is that an experienced rider can consider all the factors and decide to wait in neutral, ready to quickly shift and move out if things developed, but we believe that leaving the bike in first gear is a better default strategy for newer riders.
Reprinted from the MSF's website: 6/6/12 - https://www.retsorg.org/NewsAndEvents/MSFeNews.aspx?ar=1a415c67-102c-4e3e-8433-1367228c01d0