Regarding both (1) and (2), it seems to me like those questions might be dependent upon level design and enemy placement. I'm not sure I could give a meaningful answer without having played through the areas to know exactly how things flow together (or not). Nevertheless, my initial reactions are as follows:
(1) Would increasing the number of enemies really make a meaningful difference in the level, or would it just amount to fake difficulty? If it's just fake difficulty, I don't think I would see a need to add more enemies.
(2) It seems like you are concerned about the missiles losing their effectiveness, is this correct? If that's the case, perhaps instead of increasing the magazine expansions, would it be more effective to make the missiles more powerful? That way you wouldn't need as many missiles to get the job done in the first place. Since you would only be modifying the missiles you wouldn't be "debuffing" the enemies, but rather you would only be making the missiles a more valuable weapon.
If you are still concerned about making missile upgrades more frequent versus of bigger quantity, I would ask you about your level design. Does difficulty increase slowly but steadily? If so, maybe smaller, more frequent expansions would be in order. If difficulty ramps up significantly from one area to another, larger boosts to your missile stores might be more helpful.
Screenies are always nice.
Re: the org: I like it! It's pretty cool and I like how you've mixed up elements from music from different parts of the game. Some things to consider (these are just comments/suggestions—if you don't change anything, the music is still good).
You have doubled a lot of instruments, and I think this is mostly for timbral effect. I really like the timbre that you get when tracks 3 and 6 blend together. Very cool! With tracks 2 and 7, they often overlap, but I'm not as blown away by the timbral combination here. In some ways, I think you might be able to put track 7 to better use by making it more complementary to track 2 rather than a fairly strict imitation starting around pickups into measure 24. I like how you use tracks 4 and 5 pretty complementarily (is that a word?), and the echo effects are very effective. One thing that I think my ear would like, though, is some more long notes or pads sustaining through all of the other driving parts. You could use either tracks 1 or 8 for this, or you might be able to use track 2, 3 or 6 since they double other parts already (even though I really do like the combination of sounds on tracks 3 and 6).
Regarding percussion, I would encourage you to be careful with track R. The open hi hat sometimes seems to wash over the rest of the sounds. Specifically, I'm thinking around measure 7 and the section starting around 24. Maybe you could bring down the hi hat's volume after half a beat or so? That might keep the sounds from washing together quite as much. You've done that a bit in the section at 24, but I think you might be able to do more here. Like I said, though, I dig it already, so I'm being nitpicky. Even though I'm supposed to be writing a paper that's due tomorrow. I should probably get to doing that.
