Nice job
Ok, I have to admit very nice job. The upgrade system did work and you could see some improvements each time you upgraded something. I agree with a lot of what Cumulus Strife said, you do need to add to the game to keep people in once they are drawn in. To be honest I did get bored with it pretty quickly.
Some very good points were the smooth game play, and the cool grapics. It was a well thought out game and it played very well.
Here are a few things you can do to help it some.
1) Personal customization system. The ability to change your sub to fit you helped. You can do things like give Sub class system. Each class has a strong point and makes the player change their stratigy to match the sub they have.
2) Storyline: Defently something to help keep the player in here. Why am I after these relics and are there any body else aftre them as well.
3) Combat: This is a iffy question as the game is very good as is and there is no combat. To add it would mean more opening for classes and upgrades but possibly harder to code.
4) Abilties: maybe allow the player to gain certain abilites to allow them to do differnt things. These abilities can be dependent on class as well.
5) Puzzles: Let there be something in most stages that tell us we need to come back with a certain ability/relic/upgrade to fully complete the level.
Thoes are just a few ideas to help you along. Keep up the good work and I look forward to seeing what else you can make. :D