Mass Effect with a Personal Touch
First and foremost, love the art. Then again, you're a great artist - it's to be expected. You've designed each and every aspect of this game with brilliant style, original views and never-ceasing commitment (except that one enemy, last frog-dude, who looks like he was half-arsedly sketched, but who cares about that guy). The music was great, voice-acting top-notch (despite the phoned-in sounds) and the universe screamed of a gritty Mass-Effect (closest I can get to). It's an overall great game, but, of course, it does have a dope-load of flaws. For a first game, not nearly enough, but still - alot of them, enough to sell on Ebay.
The most pressing, annoying aspect of this game was the GUI. The thing which you stare at for 99% of the game, has to be the worst part of it. Graphics wise, it's a complete eyesore, subtracting greatly from the otherwise brilliant art and putting a nice big splotch on that game's record. You'll need to learn how to go ahead and create a proper GUI, graphics and placement wise - it wasn't only horrendous, it was way too big, too plain, and the lines used too damn big. I'll give this tutorial - it's a head start, not much and actually created with web design in mind, but it has the basics for producing a "pretty" GUI.
http://animation.about.com/od/flashan imationtutorials/ss/flashlesson22.htm
While we're on the subject of graphics, the second most horrible artistic decision in this game - the artifacting. Given that Jpegs are usually the cause of this, I'm going to give you this hint - use pngs. Disfargeg file size, because half the time I felt like yelling at the screen "What the hell is wrong with you? Never, ever, ever use Jpegs for professional quality, ever!" The risk of artifacting (that is, the file type screwing with the colours, mostly around the lines, and it's not pretty, it's not artistic, it's horrible quality and simply isn't cool. So use pngs (Gifs work too, long as you don't attempt to resize them outside of Photoshop or the like) because that just wasn't cool.
On a side note, just starting up the game again (I already played through it once) all the characters disappear on a second run-through after beating the game. Little bug/glitch, you might want to consider finding out the cause for, but not exactly pressing -game has fairly low replay value unless you're just going through for the pretty art (eh, heheh, yeah...).
Now, the universe is great. I'm seeing hints of galaxy-wide corruption, gritty tales of woe and a multitude of racism and cultural issues, all in a sci-fi tale full of toys and wonder for the geeks around here. There's no real problem here, but you might want to consider placing objects, things that have no real use in the game itself, that speak of the characters and people in this game having lives outside of the narrative while giving information on the universe that you have created. Comic books, newspapers, television broadcasts and advertising, all tidbits of the world.
On the above subject, the animation in this game needs work. Everything from movie clips (the best animation in the game was the smoke trail that the Riptide left docking the planet - yeah, not cool) to battles, all were lacking that component of flash animations and games. Seeing as you're new to this, and this is - I couldn't really be more surprised - your first game, but not your first flash, you're going to have to work on this. You may want to consider sacrificing quality for the animations, sorry. The few animations you did having stood out liek a sore thumb - as with most of the stuff that you did in flash itself.
Also, easy-peasy grinding to the point that I managed to one-shot the boss. Yeah... Took about half an hour.
Anyway, none of the above is a deal breaker. Just pointing out some issues that need addressing, and I really love this game to the point where it's all vote 5 and favourite from here. You're a great artist, author too, the plot is great and frankly I want to see more. Got some real material here, and I can't wait for Episode 2.