During the campaign, your character stumbles upon one of the element crystals in a temple, and is tempted to remove it from there but refrains. This establishes in Elemental cannon that the crystals themselves are not part of any network, but indeed are condensed magic.

So wouldn't an empire be tempted to form a scouting party to go out and physically move large crystals within their territory? This would encourage early game exploration and also allow smaller empires a chance to gain magic power even if their economy or military is week.

Also, there could be an option for the sovereign to release the magic contained within the crystal, maybe a global magic density level that would benefit all players, unlocking magical troops, causing Elementium mines to spawn, the land to heal, new magical buildings to become available (Obviously destroying the crystal would remove it from being a militarily significant capture, but to balance this and tempt players to keep it in play, the global magic level could benefit all players. This would also encourage allied nations to do such actions to coordinate the destruction or capture of such resources.

By restricting their destruction to a sovereign only spell it would also prevent players from destroying imminently captured crystals without being themselves in danger. And to keep crystals scattered within an empire to prevent stacking them in the most defensible position, maybe preventing them from being within a certain radius of eachother, or having them provide a bonus to particular resources (i.e. earth crystals providing bonuses to mines, water crystals providing bonuses to farming, air to trade and economy, and fire to city growth speed) to encourage players to scatter them accordingly.

These are just my thoughts on the matter. I'm sure other players have had the same thoughts.