That would be a really cool guitar. if you had a through neck i dont think you could have the flamed top. Supposedly through necks add to the sustain of the instrument, where as a bolt on neck can be replaced and vice versa. On a through neck if pickups are placed too close to the neck it can make it weak.
Thats all i can think of for now.
Oh i think it would be really cool if you put some effects in the guitar like a whammy switch.