Patience is a Virtue
I'm always a big fan of abstract monsters and little-used game genres, and this fits the bill for both. Whatever else I say about this game, I enjoyed myself, which is what you should be shooting for. With that in mind, some pointers:
1. Don't make your players wait so long between strike opportunities. While patience is a virtue, as is written in the title of this review, oftentimes I found myself performing a task that I already knew how to do over and over again waiting for the moment when I could actually make some progress. This is especially bad in the water enemy; I often found myself waiting through a dozen or so attacks before I finally got the chance to strike. This is not good. If the attack/move sets are to be randomized (which, judging by the fact that I sometimes got two hit opportunities in a row, they probably are), at least make the ones where progress can be made come up a little more often.
2. You're an excellent artist, but your images don't look nearly as good animated. While I'll say again that I'm a big fan of abstract monsters, there's a difference between objects-making-a-creature and objects-just-floating-around. I'm going to have to hate on your water guy again; I never felt like what I was fighting was some incalculably ancient elemental force in that battle, I felt like I was fighting bubbles. This is because it didn't really move like a living thing; it just kind of moved. Alternatively, some of the bosses deserved a few more moving parts, like the weather machine. Not everything deserves this criticism; your iron boss was great stylistically and the motion said "creature" rather than "floating stuff."
3. I know video game designers love their multi-part bosses (I know, I am one in my spare time), but players don't. Nothing is more soul-crushing than finally figuring out something's weakness and enduring a long, drawn-out battle only to have to do it all over again because the next, unknown form kills them and they have to start at the beginning. Especially for a game like this, finding patterns in behavior is critical, and to do that one usually needs more than one attempt; if even getting to that second attempt is difficult, your players are likely just going to give up. If I'm stuck on that third form and I think a few more tries would do it, but it takes ten minutes to even get there because I need to wade through the first two, my incentives for getting to that final stage are significantly less.
4. These are just minor notes: things happening simultaneously are sometimes a problem (lave spat at you while the boss is charging at you/using a fireball/ a bomb is about to explode, etc.), as is the lack of a pause button (which is really a good idea for any game) and the poor quality of the music (the same music... over and over... every thirty seconds... at least make the loop longer).
I'll definitely be waiting for the third installment, and I hope to see more improvements. If the difference in quality from the first to the second is any indicator of how the third will turn out, we'll be looking at a game to be remembered.