My favorite game.
It's hard to say which I like more. This or the original.
The appeal of the original was the scenarios and settings. The story was pretty good too.
But this game builds and enhances on the overall gameplay. The whopping number of weapon choices, each of which is very, very different. The numbers and kinds of missions enhances the flavor even more. The story is sharp enough and fitting as well.
I can't really complain because the game is executed so well, but since you guys might be pumping out a sequel sooner or later, a few points:
1) Don't be afraid to zoom out more like you do in boss fights. In fact, give the user control of how big the screen is.
2) Allies would be hot. In fact, you could even build even more diverse missions like, "escort your ally to X point" that could flavor up the missions further.
3) For some reason, getting gold stars on the "destroy everything" and "defend point" missions isn't very clear. It might beneficial to explain how to get those stars so we can play to earn them.
Great job.