There are multiple switches, buttons, LEDs, and the main throttle is a potentiometer I believe. All are exposed to water ingress. Definitely a challenge. I think it would be easiest to do what some of the diy skateboard guys are doing and take an off the shelf rc controller and stuff it in a custom 3D printed shell. Maybe some sort of silicone sealant between the halves.
Not sure what sort of sensor you would use for the throttle. Maybe a magnetic encoder wired up as a potentiometer? I know Austria Microsystems used to make an encoder that could be used like that.
For my purposes I was just sticking it inside 2 layers of Ziploc bags and trying not to fall in, haha.