For rain, waist-length jackets require better waterproofing and layers for the fly of the pants. 3/4 jackets MAY cover the fly enough so that the flaps or gussets don't have to always handle a puddle of water.
For me, no matter how well a fly is gusseted, preventing a puddle is better planning than keeping a puddle and hoping it doesn't get through.
"The belief that there is only one truth, and that oneself is in possession of it, is the root of all evil in the world."-- Max Born, Nobel Physicist