A tight game, defeated by clunky controls.
Let's get the "Clunky controls" bit over with right away. The controls don't seem to like more than two similtanious commands (ie: shoot, left, up; or shoot, down, shift) If the player gives the game more than two commands it ignores all but one of them. This is frustrating since much of the gameplay is centred around multi-tasking. I like cursor based controls, but I reccomend against following previous suggestions to change the entire control scheme. That's too much work and might create new gameplay issues. Besides, the real problem here is not the chosen control scheme, but its execution changing the scheme may just leave us with a poorly executed cursor based control scheme, which wouldn't improve the game's playability. In a keyboard scheme however, you have to structure your commands so they won't lock up. This requires copious amounts of play-testing and abusing the controls.
The "shot polarity" feature has immasculated the poor bosses. All the player has to do is shift polarity to absorb their fire since the bosses only fire intricate vollies of red and blue fireballs. A player can defeat a boss by just standing and shooting. A quick solution might be accompanying bosses with standard fighters that continue to come in waves during the battle.
Graphics are amazng. I particularly apprieciate the full cut scenes, and complete flight animations, elements too-often ignored in flash shooters. The polarity feature doens't quite go far enough to stop this game from feeling like "another space shooter", so don't count on shooter haters being converted by this game.
We, the old gamers who like our space shooters can apprieciate this one. The best feature you have however is not the polarity-shifting thingy, but your stacking power-up scheme. Unlike so many other shooters ie: Terraburst of R-Type, Polarity maintains game balance by imposing harshlimits on power-ups, but allowing them to stack. So a player can't power up their ship to the point where it becomes an invincible engine of destruction, but if she judiciously collects power-ups, she can have brief shining moments of phenominal power and she gets multiple chances in a given level to play with combinations.
Ultimately the score I have to give this game makes me sad. There's such potential here, but it's sapped away by frustrating controls, and an appallingly low difficulty level (hint: the player appears to work for the richest military star-force ever. They have a seemingly inexhaustable supply of ships to waste on pilots who can't fly and shoot at the same time. You might want to up the score needed for an extra life, just a bit). The bones are good, the enemy AI seems well doone for a scrolling shooter, and the graphics are the best I've ever seen in flash, especially in shooter games.
PS: One final suggestion, since I'm sure you're capable of doing this. A feature I really love to see in shooters is angled shooting (ie: Alpha Bounty). Adding that feature to this particular game would give the player the option to snipe enemies of a certain polarity, and make it easier to fire around other enemies, making better use of that chain feature.