[color:"orange"]being in contact with either of the substances is by itself not harmful for us.[/color]
That depends on the contact. Most humans have a relatively low resistance against water if it is completely covering their nose and mouth. Water focused through a small area under high pressure can cut through rock. Larger volumes of water can stun or knock you over (ie firehose used on rioters) and if fast enough can break bones, etc (ie someone falling off a high bridge). A bucket of water dumped on your head isn't going to do much, but if you were hit with the same amount of water fired by an air cannon, it could be fatal (you'd definitely feel it, anyway). Also, since the human body is more than half water, anything that can manipulate water directly (move, stop, heat, cool, etc) has the potential to do a lot of damage.
Most water spells are not going to have tsunami-like volumes of water, but even just switching to cold water greatly increases the damage capacity, since it can rapidly drop body temperature, tax endurance and make it much harder to defend against whatever else the water is doing, or whatever other attacks are being directed towards you. Fall overboard from a ship in the arctic circle and (without special survival gear on) your life expectancy is measured in minutes. The same fall into waters near the equator and you have a great way to cool off and a short distraction from swabbing the decks. <img src="/ubbthreads/images/graemlins/biggrin.gif" alt="" /> You could convert water spells to conventional damage and then possibly a cold damage bonus or a slow or stamina drain effect, but this would restrict the type of water spells you could have.
Freezing the water adds more possibilities for damage, since different shapes and consistencies of ice could do crushing, piercing or slashing damage. Except for cold damage or effects, most ice spells would be easier to convert to a non-resistance form than water spells.
Even with water spells, that wouldn't have to be the direct cause of damage; water (in the form of a ball, fog, pool, etc) could be used to support a summoned water creature that could attack (possibly doing poison or conventional damage, etc).
Earth magic could range from earthquakes to ripping boulders out of the ground (and hurling them at opponents) to blinding sandstorms, so it isn't hard to see how it could do damage. There is less earth in the human body than water, though, so there is less potential for damage inherently due to earth or from magic that can manipulate earth. You could consider any solid tissues in the body (or at least bones) to be associated with earth, though, and therefore at least somewhat vulnerable to earth magic directly.
[color:"orange"]even such a sistem would not be well suited to describe how boiling water will cause burns on a human, but deal cold damage to a fire elemental.[/color]
Thermodynamics explains this quit well, though. <img src="/ubbthreads/images/graemlins/biggrin.gif" alt="" />
In one of Aesop's fables a Satyr invites a lost man to spend the night in his cave. After entering, the man blows on his hands to warm them up. At dinner, the man blows on his soup to cool it off. After hearing both explanations, the Satyr kicks the man out of the cave, saying he wants nothing to do with a creature that can blow hot and cold with the same breath.
[color:"orange"]Where they have a water resistance stat it is plain normal for humans to take water damage from certain spells.[/color]
Either you call the damage done by water based spells water damage, or you use the closest single or combination of conventional damage types, and add extra modifiers to these spells for opponents that are inherently either vulnerable or resistant to water. However, elemental damage is still not going to match up perfectly with conventional damage, so getting rid of water resistance for humans is going to cause other inconsistencies or restrict water based spells.
A spell that causes ice crystals to form in your blood is going to do a lot of piercing damage, but no conventional armour is going to make a difference, regardless of how well it protects against spears and arrows. However, magic does exist in the game, so you can have some magical control over the water in your body, or (more realistically) some way to counter the spell effect surrounding you. A resistance to water magic may be an aura surrounding you which interferes with an opponent's water magic, reducing the force of the spell or its precision.
You seem to have a problem with water, earth and air damage because real humans are not inherently vulnerable to these elements. However, Rivelon is a land of magic, where humans can learn to control the elements. With control comes the ability to at least partly counter spells based on these elements, either inherently or using an enchanted object (charms, crystals, or armour bonuses). Short of some twitch based combat system where you have to actively cast a counter spell, an elemental resistance for humans seams reasonable to me. The damage done by an element may or may not be directly due to the element itself, but the defense against such a spell could inherently depend on the nature of the element.
Of course both the spell and resistance descriptions in the game needed to be worded properly. If resistances are explained in a way consistent with the game world they will seem natural. On the other hand, just having spells that do a certain type of damage and a corresponding resistance could seem artificial.
[color:"orange"]A "deep" spell system would really be a nice feature, as long as it doesn't make a mess of the game.[/color]