Good Base...

But it could use some polishing.

The story was engaging and interesting with some good plot twists, but I felt it took a little away from the flash when you had the captain "panicking" as his ships were retreating.

The flash itself had a nice style but it was obviously better on some objects than others, you could have made this so much better if you had spent just as much time detailing everything as you did the captain (although his speech was no synced with his mouth movements).

Voice acting was ok, but it wasn't spectacular. I don't really know what else to say about that.

If the flash isn't done and you know you can do better I would suggest just giving it the extra time to make it how you want it. Its not like you have a deadline to Newgrounds. Rushing really hurt the opening sequence becuase you simply took your graphics and transformed them to give an obviously flawed sense of perspective.