Two points I disagree with:
Names of the magic types
Mystical Magic? Well, it's a renaming for Arcane Magic I guess. But Mystical Magic doesn't sound as good in my opinion. Also you have the 3 classical Elemental magics, but not Earth, which is kinda strange imho.
Furthermore, you have air and earth crystal nodes (and earth and air mana) wouldn't it be more fitting to change Lightning to Air (since Lightning is a sub category of Air), Mystical to Earth and add fifth all purpose category called Arcane? (Or you can call the fifth one mystical if you want. 
)
Since you'll have light and dark (or black and white magic) for the Fallen and Humans respectively, a fifth category to place their spells in would be sensible imho.
Types of magic
Now my second disagreement is the following. This system currently sounds like the system used in GalCiv2 with the attack types and defense types, now with 4 instead of 3 kinds. I didn't like it but I can accept that you want to use a similar system.
But what I wonder is, how easy will it be to detect the kind of kit enemy units use? One enchantment is easy to display, change weapon colour or armour colour to show the enchantement. What if there are two enchantments? (Is that even possible?) Also isn't there a likely chance, that enchanting your units will get too common, making almost every unit in late game enchanted (since the only drawback is a cost increase)? One of the design goals stated was, that magic should be something rare and not ubiqituous like in other games.
Thus I'd like two things to be added:
Add a magic damage counters.
I.e. Fire magic damage against fire magic protection does less damage like you've said above. But Fire magic damage against ice protection does increased damage. Making enchanting soldiers not always the best thing to do. Sometimes using your common soldiers against a fire monster is a better idea, then sending your elite frost riders.
Thus:
Fire vs. Ice
Air vs. Earth
Mystical (or Arcane) would always do lowered damage against itself and normal damage against the others. (Light protects against dark magic and vice versa, if you see light and dark magic as mystical magic.)
Add a weapon triangle
Currently different weapons don't do that much, besides different stats.
Make it so, that
Swords/Daggers -> Axes/Hammers/Clubs -> Lances/Spears -> Swords/Daggers
(-> means left beats right; this could mean increased damage or other effects)
Armour is fine, you can add unit speed increases to leather and cloth armour, while giving penalties to mail and plate armour to balance their different protection values.
But to balance weapons they should imho be balanced against different weapons. A simple weapon triangle (or quartett is also possible but not really necessary) would give a lot more flavour to fights with mundane troops. Also it would make balancing different weapons much simplier while making the choice of weapons an interesting decision. (And yes, it's totally copied from the Fire Emblems series. But its a very easy system that leads to tons of tactical choices.)
That way you prevent the necessity of different kind of mundane damage categories while making mundane weapons still interesting without enchants. Imho an important design goal. 
(Ranged weapons like archers and javelin throwers are good against any kind of weapon of course. No modifier necessary for range weapons imho.)
I'll have a slight preference to use terms like Physical Resistance, Fire Resistance, Ice Resistance, than protection.
There is a difference between protection and resistance. Usually protection nullifies an attack while resistances do a percentage based... well... resistance to an attack. So it depends how it works.
/end wall of text
