Control over rare resources, especially mines, has escalated very quickly to the point of if your not already on a mine, your never going to be. While rare nodes should remain rare, I doubt the intention was that no new players ever see them. I propose the devs choose some of the following suggestions to improve gameplay balance of rare mining.
Rare mining shift
Mining nodes shift to new areas in their region. Current regional and distribution rules apply. The current mines collapse and new ones are formed nearby. Gives players in certain areas an opportunity to gain control over a mine until it shifts again.
Dug too deep
Each mine has a specific threshold, and once it is breached there is a chance something horrible can come out of the mine and engage whatever forces are present. Maybe it's every 5000 rare minerals mined, or less depending on the mine. NPC units engage the troops present, cancel all sov. on the square, and stay there until defeated. Would make it risky to place a ton of troops on a square, when a family of dragons can kill them all at a moments notice. Each NPC eruption from the mine would be like a mini tournament, whomever can kill all the NPC's and reclaim the mine gets to keep it. Encourages PVP without the destruction of buildings and gives a chance for established players to trade control over rare mines.
Mining Structures
New Sov. Structure called mine camp. Only goes to level 1 sov. structure. Increases the yield of the mine. You use to get 50 arterium, now your minners can get 100 every trip. The permanent mine requires you to dedicate all of your harvesters to permanently staying on the rare mine. Meaning you can harvest more resources faster, but that city can only harvest from that 1 node. Mine Camps auto ship there yields to their home city once a day. This gives good incentives for established players to focus on 1 mine, instead of claiming 5 mines per city.
Alcheologist (alchemy + Geologist)
New advancements in alchemy combined with your knowledgable geologist allow you to construct new sov. structures on mountains. New structures are called Magic Mines (please be more creative than me when naming). Magic Mines have 5 building levels. Each one producing a higher yield of a random rare resource on your sov. structure. Magic Mines eat up magic/hour aswell as other sov. costs. They do not produce the same quantity as a real mine, but allow you to get into the mining industry. They can be mined just like an existing mine.