Hmmm... I've got past the two bosses and while this is still better than anything I could make, there are a few things you could try to sort out.
If you go off screen but don't die, you can't press R to try again because you're not dead. The save point system in which you save by touching save blocks can cause problems too...
The first boss is kinda dull, since all you do is avoid his attacks for a few seconds. The second boss is better, but not great.
Overall, it's not the worst fangame I've played, but it still needs a lot of work. Sound effects, animation... oh, and turn the music down a bit.