Can only comment on the flight yoke..... it is done that way to be intuitive in the dimensional sense. Nothing to do with longitidinal accelerations. In any case if you pushed the yoke forward the aircraft will (generally speaking) go faster. All the other multitude of flight controls like throttles, mixtures, pitch, reversers, speed brakes, flaps and so on are forward for faster, aft for slower.
I can appreciate how you find it unnatural. I suppose it is a different paradigm to what you see.