Good discussion! I'm going to take liberty to answer with the “Short Version” since it's late
WoM is going to follow very much in the footsteps of MoM with regard to spell augmentation. Most spells will have a base cost and effect. You will then be able to spend more mana to increase that effect. For the moment this mainly applies to the damage a spell does, such as fireball, or how hard the spell is to dispel, such as Bull's Strength. You will be able to crank the damage on Magic Missile up pretty high, but there will be units in the game that you would want to attack with a more powerful spell. Still, you may very well run into spearmen late in the game because as they level up they will be more powerful.
I think a compromise for keeping low circle spells useful while at the same time encouraging the players to research higher tier spells would be making the cost of augmentation higher on lower circle spells. So, you would be able to get the same amount of damage out of magic missile as you could fireball, but it would cost more mana. Anyway, it's just a thought. We'll have to kick it around and work on the “scalability enigma”, lol.
Needless to say all the costs are still completely up in the air. We have to wait for the economy to take a firmer shape before we start assigning how much mana this or that is going to take.