Throttles get wet...put a plastic bag over a twist throttle if it is sitting in the rain. Otherwise cover the ingress points with your hand as you ride.
Use drip loop on the phase wires going up into the motor, so water can't run down the phase wires into the axle.
Hot motors push out hot air through the axle and anywhere else that air can get out. As they cool they suck in moist cool air from outside the motor, leading to eventual condensation inside the motor, and rusting. Best to store the bike inside after a ride in warmer air so lower relative humidity air gets back in. Or drill holes in the cover, Boeshield T9 the motor guts, and let the motor dry out through the holes.
Controllers can be wrapped in duct-tape or plastic or small dry bags.
Cut inner tube pieces about 5 inches long and tape over the end of connectors on each side, and then overlap the inner tubes when connecting the wires, so that moisture running down the wire goes over the inner tube, and not into the connectors.
Use a waterproof box for the battery, but don't forget to open it as you charge, as the BMS will need to dissipate heat at the end of the charge cycle. I use a polycarbonate Plano tackle box for my Ping battery. Totally waterproof and indestructible, with foam inside around the battery (but not the BMS) for vibration damping.
Use disk brakes if possible in the rain.