Quoted By:
Pokemon don't need to be 1:1 scaled but they should be scaled in a way that's close to their original size without breaking the game, i.e Wailord should absolutely be bigger than every other Pokemon but not so big that he clips into every building. As long as you can get the sense for the size of the Pokemon, you should be fine. GF/ILCA don't try at all and that's where the anger comes from.
HGSS also had the right idea with Pokemon being recalled if you had to go indoors or whatever.