Hands down 5/5. Before you make a sequel I think you need to seek help. I know you are a newbie in flash programming, with a storyline as epic as this you can ask an expert programmer to make the shooting gameplay even better. You can remake this to make a first 10/5 game in Kongregate history ^.^
Instead of making the sequel directly, I suggest you to REMAKE the game.
Why be epic when you can be an unbreakable legend?
Here are some criticisms that most people addressed:
1. Cutscene CGs !!! Now you only have CGs in the end game, which all of them are epic, but you will need more. Like you should put Ginny at work when she made her first mod to Deuce, or during Day 18~19, before she confront Nefretiti, and pretend to be normal when Deuce saw her. A CG of djinni bottle is a must. Oracle and Captain Gen in a red light room enjoying their last cup of tea, Deuce confronting Nef in space, where she blocks all attack, etc. Character specific CG is also needed.
2. The shooting game itself can be improved - this is artwork and I am sure you can excel.
This is a good kick to Kong scoring system!
Hands down 6/5
It will be 10/5 if there are more artworks
esp. before and after a boss battle or,
Your character meet certain conditions
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 "Epic Battle Fantasy 4"){kind=icon}
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 "The Grinns Tale"){kind=icon}
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We wish there was a 100000/5 option so you could rate us that :)