Very nice game.
This series was quite enjoyable, definitely had me anticipating when the next stage would come out. The game itself was difficult, but fun. The story was interesting, the music was enjoyable, and the characters and voice acting was pretty good. Boss fights were a lot of fun, though hard, and they all had very good and differing designs. (I have to admit it took me nearly ten deaths on the boss you fight before you get your pistol to realize it was shooting my machine gun bullets back at me when I hit it).
Mizar was a great villain to have as well, and you know you've made a good villain when you have someone playing it and cursing her out every time you fight her, especially the last fight, she just wouldn't give up.
My only compliant is the controls. Having to move while shoot diagonally, got frustrating sometimes, and since the buttons were close together, I found myself occasionally hitting the wrong button and jumping instead of shooting, or switching weapons, or etc.
The graphics weren't superb or anything, but I kind of liked it. Also loved the metroid and megaman feel of the game play. Felt nostalgic in a way.
One thing I have to say is I feel you should have made the challenge modes more noticeable. Usually after I beat the game I wouldn't return to the title screen and instead would navigate to something else. In fact it wasn't until a few hours ago, when I decided to through the game on hard, did I notice the challenge and speedrun modes and that adds so many more aspects to the game. I suppose normal people would have notices the extra modes from the locked items in the extras menu, but I usually forgot about that as well. Oh well, definitely a nice touch though and I'll be looking forward to beating all the stages on hard and in the challenge modes.
Anyway, overall a good game, I can tell a lot of effort went into this and I hope another saga like this might come out in a year or two. Until then I'll be happy with this one.