Been there, done that. I always some kind of boot. For the forward position foot pegs, I prefer a tall western style boot which keeps the wind from blowing up my pants leg. For the naked bike/neutral foot pegs where my feet are directly underneath the knee or slightly back, I prefer a hiking boot. I ALWAYS protect my ankles.
Likewise, I always wear some kind of protective layer over my arms and legs in case of a spill. I've only spilled my bike once, but I rolled (thanks to my experience from snow skiing and falling many times at high speeds) about 50 yards like an armadillo. I didn't have a bit of "road rash" but I did have a cracked rib from breaking my right side mirror off. It was an "end-over" in gravel in a very tight turn.
Oh, and gloves, gotta have gloves. Besides the obvious protection, I find that I don't have to grip the throttle as tight and I don't get a cramp in my hand.
When I see people riding in shorts, tank tops and sneakers, I cringe.:surprise: