My first idea was to give the Shards more personality. Put them in locations that are appropriate for them. And have the environment itself defend them against those not attuned to their element. They could also be guarded by appropriate creatures, that the Sovereign could take under control instead of having to kill them.
Shard locations and environment:
Air - high altitude, mountain tops, surrounded by intense winds where only strong flying units can approach them
Earth - deep underground, caves, surrounded by intense gravity that defeats anyone but the most physically strong and enduring
Fire - sea level, surrounded by flashfires and intense heat that combusts anything that isnt resistant to fire
Ice - sea level, surrounded by blizzards and intense cold that freezes anything that isn't resistant to cold
I think the Shards should be a big deal in Elemental. I think some or most of them should be in locations where you can't just pop up a city on top of them to protect them. So that fighting over them would not necessarily mean fighting over cities too. Only a Channeler should be able to claim them so there would be some risk involved in getting them. Distant Shard locations would mean the balance of power would be easier to shift late game.
My second idea was that if the shards will remain as they are now, they could start out as neutral, unaligned. Now the map generator dictates the powers any Sovereign will have, which isn't very inspiring. But if a Sovereign who comes in contact with a Shard first could choose which element to align it with, you could customize the Sov yourself. E.g. a Sovereign who chose Fire and Air powers at character creation could "wake up" a neutral shard to either of his elements of choice.
My third idea was to change the shards completely. I would actually like this one the best but it would be a fundamental change. The new four shards would also be the four schools of magic:
Elemental - the four elements, fire, air, earth, ice - all things material belong here
Spirit - all things immaterial, magical energies and forces
Life - nature, creation, healing, buffing
Death - ruin, undeath, decay, curses
The elegance of these four is that they can pretty much cover all spells imaginable. And specializations would play differently. Elemental master would be a battlemage and terraformer with a direct approach. Spirit master would be a Sorcerer / controller / counterspeller. Life would mean a buffer / healer and Death would be a debuffer raising undead armies. And of course you could mix and match to your liking.
Physically the Elemental shard could be multi-hued version of the crystal we now have. The Spirit shard would be an invisible place of Power, Life shard would be a magical tree and Death shard would be its corrupted and withered version. Life and Death would be mutually exclusive of course and a Sovereign specializing in Death magic should eventually become undead himself.
