Excellent Sequal

Weenom, you really have outdone yourself this time. I am very impressed with the progress since the first Armageddon Days!

To start off, the intro is just killer. Great story, though I can't really commend you for making it up :P The intro and menu reek of polish, I can tell you spent a lot of time on them--and boy was it worth the effort!
The look is top quality--your planets look amazing, especially with the glow that you managed to get nearly perfect on them. I LOVE the fact that shooting planets makes chunks fall off.
Gameplay is fairly standard, there isn't much wrong with it but not really a whole lot that's terribly new.

I was a little disappointed with the upgrading system, it was very confusing and didn't feel comfortable at all. I can't really see the point in doing speed upgrades and don't have enough courage to experiment with the ones past power. I notice in the screenshots on your website that you really only put powerups into power. Does this speak of imbalance? I don't have much of an idea of how this system could be improved on, but all I can really say is it took dying to figure out that I was getting powerups and needed to use them by pressing a specific button (I read the help bit, but who really remembers all the obscure button functions as they start anyway?)
Also at first the combination of the moon and hostile planets confused me quite a bit. I moved over the moon and then tried to do the same for a planet, assuming they were in the background like the moon. I then had a really terrible jumpy collision a few times till I realized it was because I was touching the planet. You definitely want to fix the collision mess. Try something like:

motion_add(point_direction(other.x,other.y,x,y),1)
if (speed>whateverspeedismax) speed=whateverspeedismax

in the ship's collision event perhaps?

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All in all, you did a really great job here. You can be sure I'll find my way back here at some point to waste time instead of studying for finals ;D