1) The only (in my opinionof course) good color that looks good as solid is a flat back, and only if you go with a monocrome look to the bike.
2) If you DO paint it a solid color, you can just buy a new sticker/graphics key from Yamaha, you can for Suzuki at least
3) Only get a Busa if you plan on some serious drag racing. Those bikes suck at handling as compared to a regular Gixxer, or a CBR. Those bikes were made for one reason, so Suzuki could say they had the fastest bike. If you really want a bike with that much power get a GSX-R1000 and get a larger bore kit, you'll have just as much power and just as sporty a bike (handling wise).
I'm not trying to tell you what to get, I'm just giving some advice from what I've read from everyone else who owns a Gixxer that I know (I also frequent www.gixxer.com). If you live in a place with mostly straight/flat roads, go for a Busa, that would be some insane power... But for me at least (because I as well was looking at getting a older Hayabusa) with all the mountains I would have been miserable with one in the mountains..
Again, just my 2 cents, I'm not trying to tell you what to do.