A very common example I see is Vec3 (just x, y, z). In proto2 you should be checking for the presence of x,y,z every time you use them, and when you do that in math equations, the incessant existence checks completely obscure the math. Really, you want to validate the presence of these fields during the parse. But in practice, what I see is either just assuming the fields exist in code and crashing on null, or admitting that protos are too clunky to use, and immediately converting every proto into a mirror internal type. It really feels like there's a major design gap here.
Don't get me started on the moronic design of proto3, where every time you see Vec3(0,0,0) you get to wonder whether it's the right value or mistakenly unset.