I've heard a lot of complaints on the forums about the difficulty of the Stormzilla fight mid-Mooshu. Having just completed the fight myself, I thought I'd offer my perspective. The fight is not impossible, but it is difficult.
I went in not knowing much of the strategy other than fire doesn't hurt Stupendor-X and to try and get Stormzilla to walk through it. Also, something about eggs. The first few round of my first attempt we spent trying to figure out what all the abilities do, as the tooltips aren't terribly helpful, though I didn't have much time to read them on the fly! Basically, you get two long range attacks, two beam attacks that will light a row of fires, two AoE attacks and two slowing abilities that will stop Stormzilla in his place for a few turns.
In my first try, I didn't realize where the fires would come from, only that they were useful, so it was a while before I even lit them with the beam attack and when I did so, they ended up being in unfortunate places. Then, I didn't destroy as many eggs as I could have, so I got a lot of little adds. They didn't hit me but they got in the way and used up the fires before stormzilla could be kited through them. I ended up fleeing and trying again (it's a long walk back, so I did not make that decision lightly).
Second attempt, my pet Tawny Turtle went over and wailed on Stormzilla a little harder than he had in the previous round and, for some reason, Stormzilla destroyed most of the eggs he was nearby with AoE attacks trying to kill my pet. Convenient! I misfired one of the beam attacks, as I didn't understand how they worked and just destroyed a building with it instead of a line of fire (by the way, the buildings drop gold if you destroy them, about 100g a piece). Quick tip: target the ground on a tile next to yourself to send a line of fire all the way across the board. Since ol' Stormy had taken care of most of the eggs, I finished off the rest. By that point, he'd finished with my pet and came after me.
I used all the attacks on him and dragged him through all the fire I could, but in the end, we were just trading blows. He got me down to about 50 health and if my last hit had missed, I would have had to start over again. Thankfully, it landed and I won. Phew.
Make sure you get as many fires to work with as you can on this one. Hopefully, it will take you as few tries as it took me!