Playing around with fire, i do not see many weaknesses, very good bless, an enchantment that can turn archery fire into fire arrows, one that makes you immortal in combat, very powerful evocation magic(Falling Fire). Is all kinda useful. Water....well cleansing water was good vs undead.
I do not know many impressive spells for water yet... I rather go with fire.
Maybe a weakness of fire is, you can't forge any good armor with it.