I agree that the efects of the 4 magic towers are not to strong (execpt the technology one) but since you can have all 4 of them with just 4 nodes and metamagic mage it seems balanced enough.
What I really would like to see is some kind of a reward for having a tower + sources of its mana.
Fe. you build tower of elements and get it's ussual bonuses. From now on as long as you control at least 1 source of fire, water, air, earth mana each, you also get additional bonus, let's say affinity to fire/water/air/earth increased by 1 to all units that already have such affinity. You will loose this bonus if you loose access to 1 of mentioned mana (by changing the node type, by trading the mana, and so on) and regeain it if you again have acces to all 4 mana.
This way you can swap the nodes to go for Tower of Mastery but you get only half the bonus from the towers (the ussual one), or you may stick to 1 or 2 of them and feel theier full power.