Had a ton of fun playing this.
My suggestions and comments are:
Time over screen took too long each time in between the loop and the upgrade page.
Gem/Heart colors were too similar to enemy colors making it visually confusing. I suggest having gems be unique colors to the ships and have all hearts red. If this is intentional to confuse the player i suggest having the enemies turn into a land mine some of the time so you punish the player for not paying attention to which item defeated enemies drop.
At one point with the mine launcher it caused defeated enemies to spawn gems out of reach from the player up in the air. This also happened once with a heart but it was close enough to be collected.
Maybe have the player kill the remaining spawned in enemies before triggering the boss fight.
Also one question:
If i have the gun set to my forward weapon and i press the gun button again, am i upgrading the gun or just purchasing the same gun over and over? Cause if so i spent a lot of time buying the same weapon over and over again lol.
Great game, I hope you add more boss fights eventually or even mini bosses.