i don't think it will be anything special i think it will gose like this
the pokemon stop/keep playing its idle animation a bight color/less light will engulf the pokemon the pokemon 3D model will be scaled down then removed the evolved 3D models will be loaded and scaled up the bight color/less light faded and the pokemon give his cry
Official Yamata no Orochi of the Shin Megami Tensei IV board NNID: Dayner, PSN: Dark_Dayner
A giant "Origin of Species" will materialize in the background, swallow up the Pokemon, then when the book opens again, you get the evolved form.
Not to be a downer, but Pokemon evolution is absolutely nothing like the implied real world evolutionary theory.
Back on topic, I assume much of the same; screen goes black with a spotlight on the pokemon as it glows and spins, gradually taking its new shape, slowing down and the glow dimming after the transformation has completed. If pokemon could evolve while in battle like in the anime, that would be amazing.
Playing) Fire Emblem: Awakening, Guild Wars 2 Waiting) Pokemon XY