You have a very amazing talent for show and not tell. It is the pinnacle of movie direction to be able to show us who they are without telling us and you actually pulled it off. I'm impressed. You got me highly engaged into your plot by peeling through the story line like an peeling an onion - teasing us layer by layer until you reach the core. And you made a badass heroine as the protagonist, which was definitely unique. And you introduced her not by telling her what she was, but by showing us via her piloting skills, interactions and conversations, and indirectly pointed out how important family is to her.
While introducing the characters and engaging us into the plot is by far your strongest and most valued trait that got me hooked, there are a slight few things you could polish.
1. The plot in itself is quite incomplete, unless of course you plan on making it into a series. So the gist is that there's a mercenary who is trying to rescue her buddies and flashes a "Solid Snake" attitude. She is on a small vessel that gets attacked by a massive ship controlled by the Evil Shy Guy Generals. While you're good at engaging us and you're very good with camera angles, the plot in itself is very shallow and undeveloped. Protagonist on mission. She gets attacked. Evil general plots to destroy world (er... mushroom kingdom). She and a group of friends work to foil it. They win. Happy Ending. The end. WOW BEST PLOT EVER! Well, okay, maybe I'm being a bit too harsh, but I do have a few pointers.
*Twists. I point this out to a lot people actually, and rarely do people take my advice, but the ones who actually do have made drastic improvements (read my reviews). For example, when you are brainstorming ideas for the plot, if it pops into your head and you're impulsed to use it, don't. It's probably been done because it's obvious. Instead, think of something outrageous that most people won't have thought of. For example, watch Larry 2, he slaps his dog with the sword and tries to get it moving, but accidentally chopped his dog's leg off. Not only was it outrageous, it was outrageous enough to make us laugh at animal cruelty AND surprise us at the same time. Another example is the Castle Series on newgrounds, especially Castle C and beyond. He killed off the main character immediately, and then showed us he's not necessarily dead. He makes the characters instead of black or white a hint of grey. And the soldiers are not cannon fodders like you make yours to be. They are elitely trained. They fight back. They know how to survive in the wild on their own.
In your case, engage a few surprise elements and hide some things away from us. Let the series start out light, and then start killing off a few characters. Or do stuff no one expects. Let the protagonist not be overly dominant. Let them ALWAYS be the underdog and the bad guys should always win 2 times out of 3 at LEAST. Or else it's the cheesy good guy kicks bad guys ass with bad guys as cannon fodders. Watch Mega man vs Quick Man for how it should be done. They should be beat up, chewed up, and near dead before landing a solid, decisive blow against the bad guys.
And let the characters be a bit more unpredictable. Make unlikely alliances from enemies, and let there be betrayal, but never tell us who. What would have given me much more respect for the series is if you let the captured shy guy be loyal to the general and say he'd rather die than betray him and the mercenary doesn't kill him out of respect because of his loyalty.
Another surprise could be to use the evil General who is supposed to be the main bad guy only as a distraction. Unveil another bad guy, a much more evil and competent one. And the sugar on top could be that the bad guy is originally one of the good guys and you never expected his or her betrayal. And good guys become bad guys. Bad guys suddenly don't seem so evil and they have a change of heart. Reveal the pasts and motivations of each characters piece by piece. You're good at that.
I look forward to your next episode! If not, I'll petition for one!