The problem with this games is that it is trying to be an iPhone game, the kind of game you check throughout the game. However, on a computer game, people want more of a game you can continuously play. I think you should decrease wait times, especially for stuff like refining. I know that it helps monetize the game to have "speed-ups" to buy, but it really interferes with gameplay
You should change the crystal system. Keep the battle fund, but you should also get crystals for each kill. Also, the amount of crystals could vary. So, if you kill the best person you get more crystals than if you kill the afk person who hasn't got a kill
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