Eh, now let's think on this:
The legendary birds are a bit too large and noble to be cute, after all, they're supposed to look severe and intimidating, like any sort of elemental beast should. Same for Lugia and Ho-oh. Nothing is cute that controls nature on a whim. Lati@s falls under this category somewhat, but the anime ruins anything it touches, especially those two. Dogs? Raikou and Entei are out; they're raggedy old monsters made to do battle. Suicune is graceful, not cute, in the same way that a cheetah chasing down an antelope is graceful but not cute. Regis? They're polygonal...and don't have faces o_O RSE legendary trio look mechanical in some ways, sometimes they seem they would fit in just fine as angels on NGE. Too cartoony and behemoth-ish to count. Gameshark quartet: Celebi = Serebii = bad memories of a certain site. Also has a prissy look on its face. Deoxys is a beast bent on killing humanity...that's always adorable (not to mention Mewtwo...pah, he's too clich? to be cute anyway). Jirachi and Mew are good candidates, just because they're small and vulnerable-looking with innocent faces. Technically the only two kawaii legendaries. My disdain for them aside, they are definitely the cutest of the bunch.