This was fun at first, but then, a few details made it rather boring, I'm afraid.
It starts with always having to start at the first and only checkpoint. You have bosses, so why not add the ability to start from their locations after you beat them? I feel like I spent 50% of the time just wanting to skip the tedious "go there, but there's rock in the way" swimming part.
Then, the enemies become tougher in large steps, as does my weaponry. This makes certain enemies become the "You need Lv6 missiles" conditions they are. I think it's fun if you have a hard time "killing Lv5 enemies with Lv4 gear", but here, hitpoints seemed ridiculous at times.
Boss enemies offer simple bullet-hell evasion-type gameplay, have too many hitpoints and - and herein lies the biggest problem - blind spots. Okay, I'll admit I've only faced the first and last bosses, but I did fine killing everything around and then just waiting until the missiles did their damage from a blind spot.
Lastly, I see that increasing your speed increases your fuel efficiency. This probably has to do with fuel usage being implemented by a time factor, not a distance factor. Thus, my attempt to invest into fuel tanks from the start was rather fruitless... Increasing your speed helps much more. I find this counter-intuitive, unless the description of rotors said something like "This greatly increases our engine efficiency", which it doesn't.
Also, as pointed out by others, the game doesn't seem tested for end-game problems. Not being able to increase projectile speed or viewing field makes it very difficult to navigate and fight with a highly upgraded submarine. After a few moments of playing, I also felt stupid for trying to shoot down enemies for money, as depth bonuses are much, much more of a reward... I don't feel I was told that diving deeper instead of swimming back for 200 Gold will net me a few thousand Gold.
And the most frustrating part of this game is how fun it is regardless of these design flaws. It shows you very well what it could have been and you try to give it a chance, pretty much like a doomed relationship, you want it to be what it isn't and hope that, after some time, it changes into what it can be.
You did a great job with respect to playability, atmosphere, sheer gaming substance and flow. I think if you took more time to design your game before you start coding, drawing, composing and testing, something very beautiful may happen!
I think this game deserves a "how it should have been"-type of sequel.