Here's the problem with your concept... you have no idea who you're audience is. If you want to make a shooter, make a shooter. If you want to make a visual novel, make a visual novel. Jumping between the slow, thoughtful intrigue of a visual novel, and the frantic adrenaline rush of a shooter leaves the audience disoriented and jarred.
It just doesn't work, as a concept. If you cut out the shooter parts of the game and added some more choices in the dialogue, I'd say this was a fine visual novel.