I would like to suggest that special buildings be required to house Global Mana Pool.
For example, a wizard tower could hold up to 100 essence, but a full blown Black Overlord Castle could house 5000. These numbers are just placeholders, of course. Also, such buildings could require crystal resources or even elementum resources to complete. THIS, IMHO, would add more depth and choices to the game. Likewise, existing buildings, such as shard shrines and temples could be used to store mana. And perhaps such buildings could be looted by enemies or roaming ruffians?
As for crystal mines. Would it make sense for such mines to generate a small amount of mana to add to the wizards stocks? Similar to mithril/adamantium and crystal mines in MoM?