Sully, Wow!, nice work mate - Ive been away for a few days so sorry for the late feedback here..
Looks great, you've done so many things right - its immediatly obvious you have put a lot of time and effort into this one. I like the art direction, simple - yet detailed if you look closely. Gameplay is a good balance between hard and fun. Lol you werent joking, those samurai tear you up! :)
I really like the way you have set the game up - Ive never thought of having a sidescroller transition to the next screen zelda style - its a really nice way to break up your stage into mini levels. Well executed.
I second Vercingetorix's opinion of only having one jump button and using the classic double jump method.
Personally, i feel that the use of the mouse is a little bit unnecessary. I would be much more at home just using the keyboard (Or a gamepad for instance). This might be different if you had to fire off ninja stars in all directions in a kind of clutch style - but from what i tested i would prefer it if when you pressed "f" you could then press up and down on the keyboard to change the angle.
(While im talking about the stars - very nice job with the gravity, its very satisfying to kill the enemy by making it arch over a hill and hit the samurai on the way down).
Nice effect with the smoke. Have you thought of allowing the player to throw them the same as the stars? (Maybe that would break the gameplay in some circumstances - but it would be fun).
My Fav HUD is the one that is similar to the screen shot you posted, but without the border on the bottom. (Im a bit of a minamilist though).
a little bug, when you swap your quick item but you have no shurikens left, it flickers - only minor but i thought id mention it.
Im curious to why you dont get good performance in IE (and ff), that could prove to be a problem. If you dont use sine grass do you get a big boost in performance? (I like the sine, but unless my character was standing still i didnt really notice it to be honest).
All in all, Well done!