I like the whole throwing potions ideas. Stock up on a bunch of them and throw them like grenades.
As far as making potions.. I hate to keep bringing Oblivion into this but they had a neat system where each ingredient had 4 'effects' to them. I believe you could combine up to 4 ingredients. If any of the ingredients had a matching effect, it would be added to the potion.
For example (using RPGWO-based effects and ingredients and changing it slightly)
Germ Weed
1) Restore Health
2) Damage Stamina
3) Fortify Blue Magic
4) Nova
Gyro
1) Restore Mana
2) Damage Stamina
3) Warmth
4) Cure Poison
Fire Weed
1) Ice
2) Restore Stamina
3) Fortify Blue Magic
4) Harm
Ok, so in combining these, the matching effects would be Damage Stamina and Fortify Blue Magic. Obviously you could remove the first ingredient and you'd get a potion that only fortified blue magic and didn't damage stamina, but that's not the point.
For each repetition of the effect, it becomes more powerful. So here, we have Fortify Blue Magic twice, giving you a standard level 1 potion. You could have 4x Fortify Blue Magic's there, giving you a level 3 potion.
In Oblivion, I think you start off only knowing the #1 effect of each ingredient and the others are unlocked if you were to discover them while mixing other ingredients. Ex:
Ingredient 1
1) Restore health
2)
(Not yet known, but it is Restore mana)
3)
4)
Ingredient 2
1) Restore health
2) Restore Stamina
3)
4)
Ingredient 3
1) Restore Stamina
2)
Not yet known, but it is Restore Mana
3)
4)
The player combines these in the hopes of making a potion to restore health and stamina, but also discovers the "Restore Mana" effect on ingredients 1 and 3 (and it is added to the potion).
Overall, this system is probably WAY too similar to Oblivion's to be implemented, but I like the idea of combining different ingredients in different ways to make customizable potions. Many times there's a tradeoff where you can make a powerful health potion but it depletes another skill.
As far as using ore as ingredients goes .. I don't know. It depends on how connected skills and attributes are. If Mining is STRENGTH and alchemy is INT+DEX .. it will be tough for alchemists to get their ingredients.
I think I'm just rambling at this point so I don't have to do work.
Edit: Lol @
faces.. didn't realize 3 "?"'s would do that. Oh well.