I dont know if anyone else has noticed this, but on the lds 767 the flap animation is modeled very well, they extend and retract like liquid, one clean motion, unlike most aircraft where the flaps extend and retract in a choppy sideshow motion. How is something like this modeled?

The flap animations are actually key frame animations defined when designing the aircraft. MS knew that flaps are different among aircraft and made it flexible that way. Choppy animations are a result of either poor design or bad frame rates. Hope this helped.