Guys, I just beat Mekadragon. Just with the shurikens. Don't give up cause it is easier than it seems. My strategy:
First and foremost, dont stop moving from one side to another, while watching for its vertical attacks and breaking as many flying things as you can, to always have platforms to stand on and shurikens to use.
Well, when the boss raises its head, it can perform to attacks: the one that electrifies the water and the blaster. If I am not wrong, it doesnt repeat the same attack twice. This is important. In these moments, stand on a platform and throw shurikens to its head like crazy. I say keep as much distance as you can, specially when it shoots at you, but also because when it goes back to the water he hurts you if you touch it.
That is how I won in the end, in a few tries.