PJ 64 seems to be worse than 1.3 in some games.... though i know it's for the better... and u can't have everything you want, but one 'messed up' ness that really caught my eye is in SUPER SMASH BROS.
In the intro DEMO, where it shows donkey kong and samus fighting, samus is supposed to fall through the moving platforms after donkey kong hits her, then she powers up and shoots and blasts donkey kong away.
In 1.3, it shows that perfectly, but in 1.4, donkey kong stays where he is, and samus blasts her shot, but donkey kong is still standing there cause samus is still on the platform when she's supposed to get down, the cool thing about it is that the camera still moves, unfocusing on the characters.