I think you should be able to have SOME control in the battles. There's not much card-game about this when all you do is watch computer-generated battles.
In Tetris Battle, another succesful energy-based game, you get 1 more max energy per level-up. That would suit this game so well - especially with the increased energy cost per mission.
Make all the card packs available through gold purchase. It's insane how much money you have to spend to get a legendary or that rare you want from these unless you are extremely lucky.