I always mean skeletal proportions when I say that. But it also has largely to do with how the body scales and animates with it.
Since the PSX days of 989 developing this game, increasing the body weight has always felt like the player just gets stretched wide. It's hard to explain, but that's just what it feels like.
Arms aren't as stubby anymore (surely everyone knows my JP reference), but the upper body is still so stocky that the arms can't wrap around naturally still.
Heads are too big, legs are too small.
Somebody a very good interpretation using Freddie Freeman and re-molding his skeletal system. I'll do some digging.
New player models is a huge undertaking, though. Every animation is tied into their current skeletal system. Every animation would have to be redone, this includes batting stances and pitching motions.