I think there were some pretty cool ideas in here! In the main gameplay loop, I liked how there were always multiple decisions to juggle, i.e. tossing rocks through clouds to give enemies less space to hide behind, and when to hide in the water vs. coming up for air. Plus, it was nice having an upgrade path, those tend to work real for these kinds of games.
There were a couple of downsides, though. One is that I thought the title screen had a confusing layout, and wasn't very appealing. This wouldn't normally be a big deal, but since the player is constantly returning to it to upgrade their abilities, it sticks out as a negative point. Plus, I was confused the first time when I started the game and already saw upgrade buttons before I even did anything. Having a separate title screen that you see once, then a different screen for the upgrades, might fix this.
I think the general ideas are pretty solid though at their core!