Is stage 2 supposed to be just a few waves of enemies and then an infinitely repeating empty stage?
Stage 1 is pretty solid, regardless, and is good enough for a jam game alone. I want to say this is one of the better entries I've played so far, but there are a few flaws that make it less enjoyable than it ought to be. My main complaint is that the ship is a bit slow. I can't zip up and down and get into a nice rhythm to destroy the enemies as they spawn. It also makes the game more memorization prone, since you're more reliant on already being in the right position as the enemies spawn.
This is exacerbated by the ship slowing down a bit as you charge. Slowing down as you charge in itself makes sense, but the narrow width of the charged shot combined with the already slow default speed makes it hard to move enough to hit the enemies. Combined with the punishment for holding the charge too long, I don't feel like I have enough time to reposition myself, and it also doesn't end up being as fun as it should.
Then there are nitpicks like the enemies that teleport into the back half of the screen on stage 2. Since the game is a bit on the punishing side, it feels cheap. Trail-and-error like that is not great in the context of a jam, where people potentially have 200+ games to play and rate, but it might have been fine in a different context.
Also, I think you can milk the bosses infinitely by absorbing bullets? You probably want to add some timers, or not give score for just absorbing bullets. One of those would solve the issue.
The contols are also a bit weird: arrow keys + space + shift. It'd be more comfortable if you had shot be at 'z' which I think is more standard?
Also, during one of my playthroughs, the stage 1 boss just disappeared and the game never advanced to stage 2.