I just finished up your game, & it was not bad, but there were a few things keeping me from enjoying it more.
I liked some of the gameplay aspects a lot. The charge shot is pretty good, & it interacts well with the homing missle enemies. Fighting them would be less interesting if you just had a generic shot. I really liked the way you did secrets, by putting them in conspicuous places and then revealing them when you get close to them without needing to touch them directly. I think my game would have been better off with something like that, to be honest. I especially liked the long ladder in a hidden area just above the beginning, next to some spikes on a wall. It felt like finding a shortcut after I found that.
Some criticisms - like some other people mentioned, it would be better to be able to take another hit or two before dying, and the run speed should be higher. I also have a personal preference for playing on gamepad, and I can use joytokey to map keyboard buttons onto the controller, but if the mouse is used I can't really do that. That's just my personal preference, so I wouldn't call that a flaw, but it is nice to give players more control options, so it's something to consider.
I did find one glitch - when I played the game the first time, everything worked fine, but the second time, for some reason the spacecraft was invisible. I could still see the counter showing how many cogs were needed & I could still interact with the platforms in the area even though were invisible. It didn't have that problem the first time I played, so I have no guess as to why it happened the 2nd time.
One other thing, the ladders were a bit awkward. There was one area with cogs near the beginning that was very hard to get to, but only because you had jump past a ladder, and your jump turned into ladder climbing if you touched it. I think a seperate jump button and up button would be ideal to solve that problem. I would also change the jump so it only activates when you press the jump button instead of just holding the jump button down. Both of those things are a matter of preference, but the vast majority of platformers do those things as I described, so I would recommend it to make players feel more comfortable.
Not a bad game once I got used to the controls, thanks for making it!