I thinks it's partially island design, with a big part of the issue coming from the way overkill is handled. Because each shot is blocked equally by a cloud absorbing it or molten rock absorbing it, I might as well surround myself with a layer of clouds, then sand, then dirt, and so on without ever upgrading any of my blocks. This makes enemy islands ineffective against mine when they attack as the first three or four volleys don't hit any of the important structures i have closer to the center. On the other hand, i have no reason to upgrade my weapons either, so I'll have like 10 cannons that hit an entire side of the enemy and after two volleys will have even the 9th realm boss's core exposed. I think if projectiles would continue after destroying a block, and maybe explosives doing splash damage, the non-dreadnought class enemies could do significant damage to island that would require more maneuvering than I tend to need, and there would be more incentive for the player to upgrade blocks and weapons.
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I downloaded the game yesterday, and have already gotten to the boss twice, though he destroyed me both times. It seems like the hardest part of the game is the first two realms and the final boss, with the rest of the game being a breeze to get through. Is there any way you could even out the difficulty of the game a bit?