As somebody said before: some sort of hitpoints / shild etc. would be nice. So its really frustrating to see all your Nanobeasts crash away.
Anyway ... this game reminds me of Parodius series (by Kanami 1994 for SNES etc.)
This game got the same upgrade system ... only that there where more BonusPowerups.
(and it was very cute and funny).
So in comparison to Parodius, your game got a loong way to go... (more and different nanobeasts with different weapon etc. ...)
Anyway ... i like your art style, your music was good too, your gameplay was okay, nice Char-Design (general / prof).
Bad points for: loosing soo many Nanobeasts (whenever i get killed), background was a bit lame (especially Stage 2), story wasn't new or very intersting - but funny.
So all in all 7 / 10, cause this game is nice and worthy to play.