Elliot is hotter, and that might be because deliberately make her seem hotter. Because we see things through J.D's point view and imagination, and it is not a secret that through all the season, whatever if they in relation or not, J.D is constantly having the hots for Elliot. So therefore, we as an audience will see more of her good sides than we would see those of Carla's. Because Carla to J.D is not just his best friend's girlfriend, she is one of his best friends and almost a sister/mother like figure to him and he doesn't find sexual attractive that much. So deliberately they have toned done her sex appeal, so we can identify more with J.D.
TL;DR: Elliot is hotter.