yeah, you've guessed it.

story wise:only in train graveyard
levels:Cloud:15-17 the most (i forgot, the laste I played the game was last night)
Tifa:10-14
Aeris:same as tifa
limit breaks:Cloud:all except for omnislash
Tifa:first two
Aeris:first two
materia:none of them have leveled up, but Cloud's orignal and the all materia are the closest to level up.
Weapons and armor:the best up to this point.